Best music, best bosses, best level design, best levels. Some people don't like the mech transformation idea, but really, it isn't necessary (trust me, I've 1CC'd it without using it), and as far as I'm concerned its only a neat bonus. Also, there's some cool scoring potential in the game. Also, the Saturn version has better graphics, sound, and gameplay mechanics in comparison to the arcade original.
2. Thunder Force IV
Great music and great boss fights. Sure, some of them can be cheap as all hell, but for the most part its an amazing game. The level design is superb, and its a bit harder than Thunder Force III (and a bit less "memorization" based if you ask me).
3. Thunder Force III AC
Slightly better than Thunder Force III because of the cool extra levels, and I find the gameplay is a bit better.
4. Thunder Force III
Awesome levels and music, and the boss fights are astounding. Truly a beautiful game regardless of if you're playing it on the Genesis or Saturn. My only problem is the memorization aspect thats in some levels... but other than that, a classic.
5. Hyper Duel - Arcade
Worse graphics, sound, and gameplay mechanics from the Saturn version. Its still a great game, but it loses a lot when you move down.
6. Blast Wind
A great straight forward shmup thats incredibly easy, but also incredibly relaxing to play. It has some of the best shmup music I've ever heard, the bosses are all fun, and the levels have branching paths. Pretty good game.
7. Elemental Master
Its easier than Blast Wind, has solid graphics, decent gameplay, and some really cool boss fights (I especially loved the fight against Roki). I ranked it low though since the music really wasn't up to par and the level design was kind of lacking. Though I do have blasting bosses with 2 shots once you get the ring.

8. Thunder Force V
Thunder Force goes 3D... and gets ugly. Aside from two levels (levels 4 and 5) I felt all the levels in this game were incredibly poorly done. The scoring system focuses much too heavily on ONE weapon, and overall the bullet patterns were just sloppy. Its an alright game, but I never felt it was anything special aside from the aforementioned levels. The music was pretty cool... but most everything else was just... meh.
9. Thunder Force II
Top down levels and extreme memorization based horizontal levels. Thats all I really have to say.
I have not played the SNES Thunder Spirits or the original Thunder Force. Though I imagine the latter would be ranked lower than Thunder Force II given the fact that it is nothing but the shitty top down levels. Bleh.