It's hard for me to believe that people would prefer the older games other than for nostalgia reasons. You can just look at the remakes for evidence of that. Crystal was my first game and I loved it...but I think I'd really rather go with Heart Gold if I had to pick between the two. Maybe if you liked the wonky mechanics and stuff in Gen 1/2 then I guess that's certainly a reason to prefer the older gens, but otherwise the newer gens for the most part are just way better mechanically, graphically, and content-wise.
I think a more interesting question would be what region or generation you prefer/like the best because that way, you can take into account the improvements the remakes made. Even then region is probably the better thing to look at since remakes would really skew how gens are viewed. For instance, 5th gen had some of the most original content in a game since the 1st gen but I would put 4th gen and 3rd gen ahead of it just because both those generations have really good remakes of some really good regions (and gen 3 had colosseum which was really good I thought but I'm leaving it and XD out because those two don't really fit imo).
If we're talking region-wise, then I would say that the "older" regions are better, particularly in terms of setting. While I'm trying to be as objective as possible here (read: not nostalgic), I feel that in general, Hoenn and Johto had some of the most memorable settings. The in-game places just felt really unique in both those games, and it's hard to forget. Places like Ecruteak and the two towers, the Ice Path, Lake of Rage, Pacifidlog town, Sootopolis City, Mt. Chimney just stand out to me as really cool locations. Kanto's Sevii Islands are also really neat I felt.
That said, I do enjoy the look and feel of the newer games
my ultimate ranking then would look something like this in terms of regions starting in last:
Kalos (unranked) - I can't really give it a ranking since I have yet to play it, but from what I've seen / heard, I can't imagine this will be that high up there. From playing ORAS, I don't like the New Mauville setup, so I doubt I'll like it in Kalos. My expectations are pretty low for this one, but hopefully I'll be pleasantly surprised. One good thing though is Mega Evos. I hated them at first, but I've realized that it allows GF the chance to "edit" certain pokemon, and for the most part I like the designs and upgrades.
Kanto - FRLG aren't bad games per say, and they certainly are part of the reason why I rate the 3rd gen so highly. But with the most recent release being the 3rd gen in like what? 2004? its age has shown. Blue is probably the second strongest rival and the Sevii Islands addition in FRLG was a really fun one, but otherwise the region itself does feel like an afterthought given that it was the original. The concept of Yellow is pretty unique though to the games and I'm excited about getting to play that in the near future.
Sinnoh - Team Galactic might be the best villains in the series I think...but the region itself just feels wholly unspectacular. From the actual Pokemon, to the gym leaders, to your rival, for a game I've probably spent the second most time on other than Ruby, it just seems all so foreign. Platinum was a really good improvement though, maybe only slightly below Emerald. But that still doesn't change the fact that the setting and people themselves just feel as unspectacular as Kanto. I couldn't even remember who the rival is in this game (I thought it was dawn/lucas...)
Hoenn - Hoenn is weird because I actually feel like Emerald is superior to ORAS...which feels wrong but it's probably true. Emerald made so many good changes from Ruby that it's really confusing to me why they weren't built upon in ORAS. The one team as the bad team in each game doesn't make sense to me and takes away from the whole two bad guys theme that Emerald had going which was really interesting. Trainer's eye is the best re-battling feature that the game have added, contests were challenging and required some thought in the original versions. It's strange that even though its the most modern game, Emerald might have done Hoenn the best. emerald Battle Frontier was really awesome and it's a shame they didn't bring that back. I guess I just almost let down by the ORAS games which is why I can't put Hoenn any higher.
Unova - I think the "reset" they did was a really cool idea and maybe even a bit underrated (certainly by me). BW2 is a game that I'm really looking forward to picking up because it seems like they really improved on BW and added in a bunch of cool ideas. Continuity with BW is also really awesome and things like the Memory Link is a nifty feature that I like because it allows for more development of ppl like the Gym leaders and what not. Cheren and Bianca aren't bad for friendly rivals, which seems to be the direction that Game Freak has wanted to take rivals. Things like PokeStar studios, the PWT, and Dream World were really interesting ideas (and stuff that I'm itching to get into for the former 2). Overall, the decision to do a region with all new Pokemon brought back a lot of the Pokemon charm and even though I don't think every single mon was a hit (looking at you garbador and vanillux) I liked the creativity and bravery they showed to bring us such a region. The reason why Unova isn't number 1 for me is 1. that the setting is pretty meh: you have the bridges and that feels like it's it (although tbf I may not have played enough to get a good feel for the region) and 2. the beginning of the games just feels way too closed off. Maybe it was just me but there were just no interesting pokemon in the beginning of the game. I hate how they force you to get one of the monkeys for the gym, and the game just feels way too linear for way too long. When you finally get beyond the second gym of BW1 and to Castelia City is when the game really takes off I think.
Johto - People might complain that Johto lacks content, and they're probably right. The plot is relatively straight-forward, Team Rocket's arc is fairly short and insignificant. But I think where Johto really wins is in its setting and characters - I've talked about the setting above, but I feel that Silver is by far the best rival in the games, no question about it. Gym leaders also are interesting and aren't so flat - who could forget Whitney, Jasmine and her sick Ampharos or Clair making you go to the Dragon's Den to get the badge? It's stuff like that make the gym leaders feel more like actual characters rather than just a roadblock in your quest to beat the league. I also love the continuity in the region. Connections to other regions I have always felt makes the game stronger and a lot more intriguing when you know the backstory coming out of R/B/Y. The Rocket arc isn't the best and most "evil" arc, but it's one that fits really well with prior events. The level curve is screwy (but that's not a big deal considering ppl complain about things being too easy). Oh, and the Pokeathlon is the best side event the games have put it. One negative is that it does feel like actual 2nd gen pokemon seem almost impossible to find, so at times it feels like you're just in an extension of Kanto. And of course, this gen has the best starters, even if they aren't the most competitively viable.
Can't believe I wrote this much on mons haha but this was fun!