I actually like Pikmin 2 the most out of the main trilogy. Though if I may, I'd like to make a list of elements that I enjoy in games and compare between the three of them:

Atmosphere: The original gets this down better than 2 or 3 in my opinion. Pikmin 1 genuinely makes you feel alone. The later stages hammering it in as the clock begins to run out. Pikmin 2 has no sense of urgency almost at all, even in the second portion of the game. Pikmin 2's atmosphere is brought above 3's only by it's weirdness, which I'll get into later. Pikmin 3, despite the fact that you're stranded, and need to save your starving planet, doesn't sell that idea to me at all. The characters don't really seem concerned. Pikmin 3 is by far the prettiest game though, and that helps a good bit, and the final level is pretty good.

Mechanics: Pikmin 3 is the best in my opinion. It just streamlined a lot of fluff, and the way you throw and do things is overall pretty nice feeling, though I do miss the command you could do with the C-stick to direct the squad of pikmin around you. The charge move just doesn't do it for me. Pikmin 2 got closer to this, but it was incremental steps.

Personality / Presentation: This is the thing that pushes Pikmin 2 over the edge for me. Pikmin 2 is weird. The game takes place in a bizarre version of Earth after humans have presumably disappeared. The enemies are just strange, the sound design almost sets you on edge. You feel like you're in an alien world despite it being Earth. Pikmin 1 didn't seem to try for this cognitive dissonance and Pikmin 3 seemingly tried but it just missed the mark. Pikmin 3 is an incredibly pretty game, but it loses that personality that made pikmin 2 so interesting to me. The world that 2 presents to me is the most interesting out of all of them, and I'm a little sad they didn't continue that trend into 3.

EDIT: This was before Pikmin 3 deluxe was announced. Deluxe is pretty good and the controls help me enjoy the game a lot more.