My personal thoughts on the matter
Gen 1: probably my least liked generation. I don't have a lot of love for the Kanto region due to a lot of the areas feeling bland and bad dungeon design (cough Rock tunnel cough). I like most of the Pokémon designs and the gym leaders are some of the hardest I have fought (due to other reasons). I honestly don't like Team Rocket because they don't strike me as a evil organization and more of a pathetic group of thieves. There is nothing avidly wrong with the games, but the other generations do what Gen 1 did a lot better.
Gen 2: It fixes a lot of the problems I had with gen 1. The region feels more lively then Gen 1 and the region as a whole is more exciting to explore. they nailed the time period of Kanto to make it feel similar but different. I like the new ways of catching and training pokemon (not including the trade evolutions but that was also a problem in gen 1). Team rocket actually feels worse than they were in gen 1 however I still prefer this over gen 1.
Gen 3: The generation I came into the series. The Hoenn region was designed to be separate from Kanto and Jhoto and I love most of the changes (the exception being the sea routes). Team Magma and Aqua feel like a threat, unlike team rocket and I love the plan that they have in the games. especially emerald where both are in the story. I love the designs for the Pokémon here because again, it differentiates itself from Kanto and Jhoto. I will admit that the national dex is a pain in this generation but the national dex is something I don't care about in this generation. The soundtrack (which is something I haven't brought up in the other gen's, I love 8 bit music and I enjoy most of the tracks in each) I love, especially considering that it is on a GBA. My only other complaint is the graphics, they took out animated sprites for ruby and sapphire, which I can only explain as lack of cartridge memory, and the fact that the over world sprites in R/S/E look worse then in FR/LG (probably because they didn't want to make new sprites but still...)
Gen 4: Gen 4 fixed some of the problems I had in gen 3 (less water routes) but in D/P they made another problem, the surfing speed . I still enjoy going through Sinnoh even though I think they went overboard with the legendaries and their powers but I still enjoyed the designs of the new pokemon. I enjoyed the ancient theme of the game and team Galactic as, once again, they have a good plan. I also don't like Mt Coronet as a dungeon because of the amount of HM you need to use (but I still prefer it over Mt Moon). The soundtrack is mostly forgettable in my opinion (the exceptions being Cynthia's battle theme, team galactic, Route 201 and 209 off the top of my head). I see where people are coming from, that gen 4 is the worse generation out of all of them, I just don't think that it deserves all the hate that it gets.
Gen 5: Gen 5 is very hit and miss for me. I have grown to like most of the designs (still don't like Enboar and Garbadoor) but I do like the region itself. the dungeons don't feel tedious to explore, they idea of city and country works well and I love how each gym feels drastically different from any other (something that they have been doing since gen 1 but it is more apparent here, love the soundtrack, but my biggest problem is Team Plasma. In Black and white, they have a good, unique plan. "Guilt the trainers into releasing their Pokémon and take over a helpless region = good plan. In black and white 2 on the other hand, I think they went back a step and I don't like the new team plasma as a result. I like the confrontations with N because, unlike the other rivals from other games, you cant really predict what he is going to use. I also like the idea of the dream world and the Entralink so I hope that they bring those back.