I dunno, it's serviceable as far as plots go. It is all over the place, though, and there are way too many characters with nonsensical plot ties. (Spoiler: The shadow government stuff is pretty silly, but that always is...) Their use of terms and concepts from physics and philosophy of time is completely off the wall though, and I don't think it's just that things were lost in translation, but rather that they slapped a bunch of technobabble together without understanding any of it. For example, it's alleged at one point that reality will be sucked into an alternate dimension, which will destroy reality.
At least they didn't pad the game out far beyond what they could have (although this is maybe a good and bad thing, because I'm sure I will soon tire of the six scenarios; if it was a better game then this might not be so much at issue). I'm at the beginning of the last episode and I am pretty sure this isn't going to get tied together in a satisfactory way. But at least they keep the new stuff to memorize coming at a good pace, right?
I like the basic idea of having the player go through and see that things have changed after dives into the past, but not only was it not really used that well (there are some attempts at Groundhog Day-ishness but it's not a lot), they decided to break with that too early on - plus any time changes get lost in the emotional drama crap that again wasn't tied in there. Oh look, I'm going to have a dramatic final word while I phase out of the timeline! Complete with going sparkly! Your only sense of what is happening to the world at large (which is what I found most interesting) is by reading through the bundles of text at the computer monitors, and re-reading it over and over again each time there is a "New" tag next to the entry.
Lots of little blunders, but I don't think they're really fatal.
Parasite Eve is pretty close to this game in many ways, except it doesn't have the cool Feats (Achievements for unlocking shit) system, but instead has junk collection. Both systems have some really stupidly designed grinding mechanics, i.e. I've basically run out of ammo in the original game because I didn't realize that stacking a ton of Burst powerups to a submachine gun will basically destroy its effectiveness. In this game, you have the DNA plots, which is a cool idea except that you start to realize that the chance of getting upgrades to two or even three item slots at once decreases at a wild rate: Going from two level 1 abilities to two level 2 abilities of the same type, with a level 1 chip, means you have (ignoring mutation) the chance of either ability slot ending up at 0, 1, or 2 - 9 possibilities, or roughly a 1 in 9 chance of hitting it. Going from two level 14 abilities to two level 15 abilities (ignoring all the complications) would give you 15*15 combinations...and of course this is ignoring the fact that even if you have a DNA chip with the same abilities you want (not likely), it can mutate. If you don't have a chip with the exact right abilities in the right spots, it is very likely that you will retain the desired ability a mere fraction of the time. I've seen the Rapid Link ability a few times and I am starting to kick myself for not getting it, because pressing the button hundreds of times while leveling with 10 chips is better than not having the right ability. Unfortunately this all seems unavoidable if you want to have a good DNA board with high-tiered abilities.
It's almost as bad an OCD trigger as Vagrant Story's stat wines causing me to load (which I shouldn't have done once I realized I was way overleveled and there's no need to put extra wear on the game's laser for a few more stat points per wine, but OH BOY PROGRESS! Gotta hit that 999 cap!

).
I couldn't say whether 3rd Birthday's BP weapon upgrade unlock system (ignoring the feats) is better than Parasite Eve's weapon combination system, except I will say that while it is nice in theory to have the option of altering a weapon in 3rd for more impact or power, in reality these changes seem minor and the basic stats of the weapon have already largely determined its role. The AK-47-alike (the T54) is not going to take the role of the impact-focused SWAT carbine.