Probably not a popular choice, but my favorite games in the series are 4 & XF. The combat system in 4 is fantastic and has a lot more depth than any of the previous games and I like the characters better than the similar one used in 5. And Wild Arms XF is easily one of the best FFT-style SRPGs ever.
Though to be honest, I'd be fine with a Wild Arms 6 that was similar in style to any of the previous games. They all have their strengths.
I agree that XF was awesome (and overlooked by too many people), I was completely hooked on that game for a long time, I love how they really tried to do something different within the confines of the genre. Actually, I think that's one of the best things about the WA series in general, they're not afraid to go a bit crazy with game systems and such. I mean, even if I consider 4 to be the worst game in the series (sorry
), I really appreciated all the new and crazy stuff they tried (like the HP/MP meter you can adjust, for example). I always felt 4 was like an experiment within a limited game, where 5 was the results from that.
I still consider 1 and 5 to be the best ones, but hell, I like them all. As long as they bring out a new one, I'm there.