Hmm, looking at the poll it is pretty darn even overall. Gen 3 is ahead (not too surprising, it is the gen seemingly with the most nostalgia going on over it right now), but everything else is close. Gen I even not too far behind, and there's not exactly much games in that gen to represent it either.
I won't deny that nostalgia is a significant reason for me going with gen II. But dang it, out of all the tunes, there's more memorable ones and ones I just enjoy listening to, looking at sheet music of, etc, from GSC than any other game.
Gen III would be my second choice though, and to be honest it's not because of the main games. There's a lot of nice tunes in RSE, but that trumpet sample? Pretty poor (and it being a GBA isn't an excuse, look at the likes of other games using trumpets or brass in general. Mother 3 comes to mind as a game with pretty good trumpet sampling). As it is, BRAAAP-BAAAP-BAAAAP-BAAAAAAAP is a common joke of the 3rd gen games these days.
And FRLG didn't do a very good job imo on the remixes, overall. Some were nice, but a lot were lacking. And the new tunes didn't do much either, unlike say the HGSS ones, of which I liked the new additions (e.g. Safari Zone).
But why I would put 3rd gen as my 2nd choice would be because of the spinoff games in Colosseum and XD. Genius Sonority have made a lot of good tunes thanks to Tawada (even if some didn't fit situations too well... looking at you, overly cheerful Cipher Lab theme and XD Wild Pokémon Battle theme). And really, a gen which brought us both of Miror B's theme? That's worth a lot right there, haha.
4th gen - HGSS did a good job with the remixes, personally. DPPt had some nice themes too (e.g. Cynthia themes, that one snow route theme, the rival battle theme). BW was mixed - bar route 10 (amazing), I didn't get too found of the route themes. But some battle themes were quite nice (well... heck, most were), and town themes was where it shown best. Looking at you, Driftveil.
6th gen - nice to see a step up in the instrument sampling, and there were some nice takes on say the Gym Battle theme. But not really as memorable as other games, but I'll put that down to the games only being <half a year old. And there's always the whatever-is-the-next-gen-6 game to enjoy too.