Here's what I got so far. Three remarks as a preamble:
- In case I forgot to add it somewhere: every value has autofire in mind.
- It seems obvious to me that this guide did not have a lot of scoring in mind, and not only because of the vague nature of defining it as pegboy rightfully pointed out. For example: two of the lowest ranking games are Insector X and Gekirindan (both with 3 points). I would agree with that sentiment, but only for survival. When you play Gekirindan for score you're not allowed to lose a life or to use a bomb while forced to painfully milking some bosses for an extended period of time which can get pretty tricky since the hitboxes are quite big. Insector X's scoring consists of repeating a laughably easy checkpoint over and over. So there's no question which one of the two would be much harder when played for score. There are quite a few similar cases throughout, I just cite this one pars pro toto.
- As always, this is not meant to be objective in any way. Everyone has certain strengths and weaknesses thus it's not easy to matter-of-factly find valid arguments that'll be universally applicable. This is merely how I personally felt about those clears.
These are the games that are ranked too high:
41: Twin Eagle: Revenge Joe's Brother. According to this document, Twin Eagle is one of the hardest games out there, especially among the games without additional loops. I can partially understand why that is, it's extremely exaggerated nonetheless. If you use an autofire rate that is about 15Hz or higher the game indeed becomes impossible. It's also one of the most inconsistent games out there, anyone who claims that he's able to beat it consistently is lying. Even if you hypothetically were the best player on earth there's simply nothing you can do when bad luck strikes during the chase sequences. You sometimes dodge incoming shots by moving to one side only to get immediately murdered afterwards by a plane that materializes right behind you. If that happens you're severely underpowered and way too slow for the next stage and might as well reset. The actual stages themselves also have some nasty tricks up their sleeves, the anti-air missile tanks are a colossal threat if you don't know where there are and how to deal with them. Lastly, this is one of those "hitbox 'em ups", where you have to learn how to steer an oversized tin box. All in all a tough game, and one that will demand a player to spam runs even after having studied all important facets. But it's not inherently demanding enough to be this high up. I'd give it 24-26 points, depending on your kusoge tolerance a little bit more.
40: Mahou Keibitai Gun Hohki/Mystic Riders, 2-ALL. Now this one comes with a certain caveat. It is an Irem 2-ALL and as such a veritable challenge. I'd argue that it is not as tough as an Image Fight 2-ALL or an R-Type II 2-ALL, however (which are ranked with 36 and 34 points, respectively). The latter games are much more unforgiving since their second loops are not only extremely hard in general terms, but also feature brutal checkpoints (especially R-Type II). In Gun Hohki you don't have checkpoints and respawn with full power provided you have enough crystals in stock. Now, that doesn't mean you can't lose all your lives in a snap, particularly the second loop's final stage can empty your entire stock in a few seconds. It is generally more lenient, however. My caveat stems from the controls: it is paramount to learn how to constantly and wisely use the spin manoeuvre that'll grant complete invincibility for a while. You cannot hope to beat the second loop without it. I wonder if it is harder to consistently perform this move with arcade controls, I find it not too bad with the regular Xbox 360 pad I'm using, I can imagine it being more tricky with a stick. Since you have to chain this stunt several times in a row it's important being able to reliably pull that off. After all is said and done I'd give Gun Hohki about 30 points, placing it between an R-Type II 2-ALL and an R-Type 2-ALL.
35: Space Battleship Gomora/Uchuu Senkan Gomora/Bio-Ship Paladin. This is an odd one. The entire game is fairly trivial, then you hit one of the most unsettling final stages (including the boss) in existence. It's a relentless damage race where you have to do just the right things or die in obscurity. The final boss will kill you at least once since the game is simply designed around that fact, and thanks to the health system you also will reach the final boss with merely a sliver of health under ideal circumstances (the more health you have the bigger your ship is, yet only a small ship can evade the laser barrages of the enemies in the stage). You have to meticulously study the stage and learn to move your oil tanker of a vehicle which is a challenge in its own right. I would almost say, however, that this stage can be consistently beaten unless you get really unlucky with the auto aim in the beginning of the stage. It's always going to be close, no doubt. Overall I'd give this one 24-26 points just like Twin Eagle, again with a certain tolerance. I find those memorizers with awkward, huge hitboxes to be much easier than fast, frantic games, but I know some people are the complete opposite when it comes to that.
27: P-47: The Freedom Fighter (with autofire), 1-ALL. This actually is a frantic vertical shooter in disguise of a hori, but it is not too bad. Several extends are scattered throughout the stages, bosses are fairly simple, recovery is always possible. The last stages get pretty rough, you're going to have a generous cushion of lives if you play it right before, though. Moreso a case for the low 20's.
25: US AAF Mustang (with autofire), 1-ALL. The same applies here, except that it is for the most parts much easier than P-47, albeit with a stupid final stage that will decimate your resources. Overall still a fairly manageable game, I'd say about 18 points are adequate.
22: Strike Gunner S.T.G (with autofire). This one I don't understand at all. You simply cannot die in the game and you also have to know which special weapons to use in which stage, other than that it is really simple. The entire game lasts for less than 15 minutes and there's only one dangerous boss fight, everything else can be taken care of with rudimentary movements and the special weapons. Even if you take into account that figuring out which one you have to use might take a while there's not much in the way of dangerous occurences in the game. I'd actually rank it together with some of the easiest games, 5 points or so should suffice.
18: Heavy Unit, 1-ALL. No way this is on the same level as an R-Type or Image Fight 1-ALL. There's one ridiculous section that might randomly kill you, the rest of the game is pretty trivial. The hitbox is astoundingly small and the shield withstands several hits before it finally deactivates. Checkpoint recovery is admittedly almost impossible, outside of that one part that shouldn't be much of a problem. 5 points for this one, too.
16: GunNail (with autofire). Very generous game when not played for score, you get tons of bombs and health. If you use your resources somewhat smart there shouldn't be a single stretch where you have to do much in the way of actual execution. I'd give it about 8 points.
14: Sand Scorpion, 1-ALL. Child's play if you know about not powering up all the way, even without the bomb glitch. Every part that could be minimally tricky is plagued with crippling slowdowns. 3 points.
Games that are ranked too low:
30: Raiden II (with autofire), 1-ALL. This objection might partially be based on my difficulties with frantic games, yet I firmly believe that Raiden II is an excruciatingly hard game. And it ranks 4 points below Zing Zing Zip which is kinda-sorta similar in its difficulty (not quite since ZZZ is a resource 'em up while Raiden II is moreso conventional) which I find to be just wrong. If you die anywhere outside the final boss you can almost certainly kiss your credit goodbye. Your ship is very slow, the bullets are insanely fast. Stage 3 of Raiden II is already much harder than most games ever will get, and it only gets meaner from here! I'd give this probably about 35-36 points, I dare say it's about as hard as some of the toughest Irem 2-ALLs, although not as grueling as the Xexex 2-ALL which also features lighning-fast projectiles.
24: Salamander 2 (with autofire), 2-ALL. While the first loop is indeed not too much of a challenge, the second loop is a lot more demanding, namely 2-5 and 2-6, and chiefly the final boss. You can lose a great run due to one bad suicide bullet or tiny error at any given time and since it is strongly advised to play at full speed you're prone to make desastrous input mistakes; it's just an overall hectic, chaotic game. Losing at least one life before starting the loop helps, but you still have to battle enormously aggressive enemies by the end. Playing for 2 loops in general means that you have to stay focused for quite a while. I'd rank this together with a Gradius III 1-ALL, which would mean it gets about 30 points.
12: Dragon Saber. This just might be the most nonsensical choice on the entire list. This is a mean game throughout, it's fairly random as far as the power-ups/extends are concerned, you have to have precise routes for later stages and decent strategies for the bosses, and the final boss as well as the checkpoint leading to him are very tough. I'll concede that checkpoint recovery in general is feasible anywhere (provided you get a good set of power-ups), that doesn't mean it's easy, though. The game is especially nasty at high rank, I don't see myself ever beating the final boss with the lightning dragon. I'd give it about 26 points at least, if not more.
6: Dragon Spirit (with autofire). Almost as silly. Spirit is much easier than Saber, but not that much, and it's most certainly not in the same general category as Thunder Cross or a Life Force 1-ALL. 16-18 points.
I'd also argue that E.D.F. (23), a Parodius Da! 1-ALL (24), Rezon (26) and a V-V 2-ALL (32) are a bit low compared to some of the other games in those regions, but they're not ranked so low that I would outright contest their placement, it's moreso that it feels wrong in relative terms.
Bonus 1: Games I haven't cleared yet but where I can say with certainty that they're placed too low:
25: Sexy Parodius (with autofire, including special stage). I cleared this game without the special stage and with a terrible score on the PSP, so I can attest that the 15 points for a survival clear are somewhat reasonable. Considering that you have to play very well in order to even see the special stage, let alone beating the darn thing, this seems to be gravely wrong. The special stage is akin to the most difficult stage in a high loop of a regular Konami game, and since Sexy Parodius will eventually throw suicide bullets at you, anyway, that is saying something! Probably at least a 30, but not nearly as ridiculous as...
23: Gokujou Parodius (with autofire, including special stage). Yeah, right. Goku Paro is even harder than Sexy Paro, and the special stage here is ridiculously hard. Surely in the low- or mid-30's, at least. 13 points without the special stage is also way too low (I've done that, so this is a less speculative statement), it's easier than Parodius Da! this way when not played for score, but not that much. This is still a perfectly sane argument compared to...
14: Same! Same! Same! (with autofire), 1-ALL.
I'm going to assume they mean the 1P version since nothing else is specified. I see Same! essentially as a Psikyo 2-ALL, only in one loop. First half of the game requires systematic knowledge of the general gameplay mechanics and level layout, second half is where all hell breaks loose and bullets are just blurry schemes since they move so fast. Checkpoint recovery might not be as bad as it is in something like Gradius III, yet it is still ludicrous. This game is easily at the high end of the 30's. I can only hope they mean the 2P version or something.
Viewpoint seems also too low, I can definitely say it's harder than one loop of the first R-Type due to the perspective and the devious bosses, a 14 doesn't reflect that at all.
Bonus 2: Games/loops I've cleared that are not present on the main list (every game with autofire, of course):
40: Tatsujin Ou (-4 for Truxton II)
30: Gradius II, 2-ALL
28: Gradius, 3-ALL
28: Salamander, 3-ALL
28: Life Force, 3-ALL
24: Mr. Heli no Daibouken
22: Salamander, 2-ALL
22: Life Force, 2-ALL
20: Gradius, 2-ALL
20: Mad Shark, 1-ALL
20: Skull Fang, Chase mode, Japanese version
18: Kiki Kaikai, 1-ALL
15: Pulstar
15: Forgotten Worlds
12: Sky Smasher, 1-ALL
10: Hellfire (1P version, 2P version is even easier)
8: Exzisus (for the Japanese version, -1 for the US version; 20 for a 2-ALL of the US version)
2: Scramble, 1-ALL
And that, as they say, is that! Will expand upon this once I got more clears under my belt.