A lot of my favourites aren't big in the competitive scene, but I don't really play in the competitive scene so that's ok by me. I like pokemon for what they are, not for how many wins they'll get me
Gen 1: Alakazam.
It takes a lot of effort to try to catch a damned Abra, unless you're adequately prepared, and it requires a trade to fully evolve, but the payoff is worth it. Alakazam is a glass cannon, through and through. It's fast and has very strong psychic attacks, but its also very fragile. An overpowered king of the overpowered Psychic type back in Gen 1, still quite strong to this day even after Psychic was balanced. To top it all off, I love how he looks aesthetically, he really embodies the Psychic type.
Addendum: I'll also include Eevee as tied for first for Gen 1. I love all of the Eeveelutions to death, and though Alakazam outshines Eevee and its Gen 1 evolutions (only barely on Vaporeon and Jolteon though), later Eeveelutions are my absolute favourite, shout outs to Espeon, Glaceon and Sylveon, but that'd be boring to list the Eeveelutions for half the generations, so I'll just compile them all here under Eevee.
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Gen 2: Crobat.
I always loved Zubat but Zubat and Golbats use in Generation 1 was... dubious at best. Gen 2 changed that. While Zubat and Golbat were still relatively useless (they are considerably more powerful today), Crobat was a beast, a beast who just kept getting better as the generations went on. Crobat is my go-to Flying type, and with the advent of Faerie types, his Poison type looks a lot more desireable, too.
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Gen 3: Mudk- no. Not him. This one is a difficult tossup between Altaria and Gardevoir.
On one hand, Altaria is a beautiful Flying/Dragon type with a bit of bulk to him, and I'm quite looking forward to his mega-evolution in ORAS. On the other hand, Gardevoir is my go-to Psychic, even more so than Alakazam, due to the fact that she's not only powerful, but she's a decent bit bulkier too. Faerie type complements her very well nowadays but even before then she was a powerful psychic type to use.
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Gen 4: Another tie between Vespiquen and Froslass.
The designs of both are aesthetically pleasing to me, both of them look unique and even sort of elegant in a way (in a weird sort of way in Vespiquen's case). Vespiquen is difficult to obtain, especially a Shiny variant, due to only evolving from a female Combee, which is very rare. I enjoy how bulky she is and how she has several signature moves no other pokemon can get, which sort of ties in to how bulky she is. As for Froslass, Ice has always been one of my favourite types despite how badly it has it in type matchups, and an Ice/Ghost type is a unique combination which I enjoy. She's also somewhat difficult to get, but a female Snorunt is easier to find than a female Combee. She has a nice set of attacks and, well, she's just awesome imo.
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Gen 5: Cincinno and.... Garbodor. No joke.
Cincinno is cute, and doesn't feel like it'd be overall useful, and yet with the right ability it has a very fun moveset. Technician or Skill Link both tie in well to its very nice variety of multi-hit moves, Rock Blast, Bullet Seed and Tail Slap. This makes it a nasty sweeper if you can get it the stats it needs, since the combination of Rock, Grass and STAB Normal gives Cincinno a lot of choices. As for Garbodor... I initially hated it, I thought Trubbish was kind of cute while Garbodor was a nasty mess, but it grew on me over time. After a while I decided to actually use Garbodor. It reminded me a lot of Muk, who I also loved, and I found him fun to use. Now, Garbodor is one of my top picks for Gen 5.
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Gen 6: Greninja and Helioptile.
Greninja is the only Starter final evolution I really truly loved. I love a lot of the first stage evolutions on starters, like Squirtle, Totodile and Treecko, and while I did like some of the final evos, I never really LOVED them. Greninja was different. I always knew from the start, before we knew anything on XY Starter evos, that Froakie would be the one I'd choose. Then I saw the leaked image of Greninja, and... I was disappointed. I heard that it was better in action rather than in that one still low quality image, but I just didn't see it. I was disappointed that it was going to be a ninja, for a start, and it just looked weird in that image. I was wrong. Greninja turned out to be an amazing pokemon with a very unique moveset, and it was beautiful in action. I am now pleased with all of Froakie's evoltions, and I couldn't be happier to have Froakie as my starter.
As for Helioptile... I'd just like to point out that Helioptile is my personal Pikachu. I think it looks absolutely adorable, and I refuse to evolve it Heliolisk. I just don't like Heliolisk. So I slapped an Eviolite on my Helioptile and took it with me on my first run through XY, and absolutely loved it. That thing single handedly took down Lysandre's Mega Gyarados, despite it being Water/Dragon, thus losing all of its weakness to Electricity, and his Gyarados knowing Earthquake. Clearly it wasn't as strong as what it COULD have been, but it really impressed me, and now Helioptile is officially the only pokemon I would never evolve.