Out of those which I've player, Mystical Power Plant is the best. The effort put into making the story and characters seem so canon-like, the stunning visual effects, the playable roster, level-up system and the stunning soundtrack make it more pleasant to play than the official games. The CAVE mode is awesome too. I'm taking into consideration the game is not yet complete and there is an extra stage to try too. The only issue I have is some patterns being downright impossible before you memorize them, such as Momo's final card or Tenmu's square.
Marine Benefit I played less, but that one is also very creative both with shot types, original characters and soundtrack, all while keeping the marine theme intact and varied. It's much less polished than MPP by virtue of some shot types being crap (SanaeC) and some being able to break the already lenient and moderately creative resource system in half. Oh, and Kasumi & Megumi battles are hella fun, but it's kinda balanced by Mikoto being way too piss easy.
Concealed the Conclusion is pretty meh on patterns, but I give it tons of points on the grounds of multiple routes and the soundtrack, especially the CD themes. And the story is just incredible.
Never got to play The Last Comer myself, but it's right there with MPP in terms of soundtrack and the game's take on the Christianity theme is just mind-blowing. From what I've seen though, the star barrier system breaks the game pretty bad :ohdear:.