Depends really, if you freaking love Gundam Seed like me ZAFT 2 is the best, it's an expansion pack of ZAFT.
Me:
ZAFT 2
NEXT
Most people:
NEXT
ZAFT 2
Don't bother with the older Z-Gundam Titan ones. NEXT has less Gundams to pilot than ZAFT 2 but is across all different Gundam anime and was absolutely huge popularity-wise.
Please note: This is a 2v2 game, the arcade mode can be fun but that's not where the greatness is. You need to play it 4p, which means 4x System 2x6 (or 256 for NEXT) in a LAN. High barrier I know but once you get into it you'll realise why it's been consistently top of the Japanese arcade charts since ZAFT came out. Kinda like if you experienced 3s arcade 1p you might think it's ok, but when you play 1v1 you're playing the real thing and it'll suck you in for years.