Well, there are a few of these that stand out:
--I like Machop better than its evolutions because first of all, it's cuter (no offense, I think it's evolutions are kind of ugly), and it also seems more lively and less aggressive or ostentatious as Machoke and Machamp seem to be. Machoke and Machamp are just... too muscular for me.
--I like Dragonair better than Dragonite--in fact, Dragonair's one of my top 10 favorite Pokemon! Dragonair seems more mysterious and certainly is more beautiful than Dragonite. From the looks of things, it ought to have more magical power than the raw strength that Dragonite has, and since magic is what I like, Dragonair's my buddy. And the whole thing about changing the weather--pretty neat huh? And those blue orbs are so pretty... Dragonite just looks too over-powerful to appeal to me, or at least not as much as Dragonair by a long shot.
--I like Psyduck better than Golduck. However, if it weren't for the anime, that might change... Psyduck is soooooo funny in the anime--the whole thing about headaches and psychic power and Misty's frustration with it... Psyduck is dumb, true, but in a wonderful and, um, "intelligent" kind of way.
--I like Haunter better than Gengar--in fact, I'm always reluctant to evolve my Haunter in the game. Haunter is much scarier and more "haunting" than Gengar--Gengar just seems like a prankster with a few gags here and there. But I guess part of what enhances this is the anime episode "Haunter vs. Kadabra"...
--It's a close call, but I like Kirlia better than Gardevoir. Kirlia seems to be more in tune with the psychic world, with the ability to create illusions, the amplifying power of its horns, etc. It just looks so graceful yet a small touch of sinister--just what I like in a Pokemon. (By the way, Kirlia is my favorite existing Pokemon.) I think Gardevoir's too caught up in protecting its trainer and such to live up to its status as a psychic Pokemon... so Kirlia jumped ahead.
--I like Goldeen better than Seaking. Goldeen is much prettier and just more interesting, especially since the anime came around.
--I like Whismur better than Loudred and Exploud--it's so cute!!
--I like Smoochum better than Jynx--IT'S SO CUTE!!!!!
--I like Skitty a tiny bit better than Delcatty, not just because it's so cute, but because of its funny playful personality, its tendency to chase its tail and go wondering off... May's Skitty just lights up the Hoenn section of the anime!
--For the same reasons as Skitty, I like Torchic and Spheal better than their evolutions.
--I think Barboach is way more adorable than Whiscash... Plus, I grew fond of it when I had a Barboach in Sapphire what won the Master Rank Cuteness contest... I even refused to evolve it afterwards!
--I like Slowpoke better than its evolutions because, well... I forgot. XD
--I like Magikarp better than Gyarados--it's so funny when it's weak, and there's much mystery behind it despite that... whereas all there is to Gyarados is a raging brute.
--I like Koffing better than Weezing just because in the anime, it had more heart, especially with James...
--I LIKE JIGGLYPUFF BETTER THAN WIGGLYTUFF! So cool with the way it puts its audience to sleep then gets angry and draws on their faces...
--I like Larvitar better than Pupitar and Tyranitar because of appearance, and also because of that touching few episodes involving the poor Larvitar that lost his mommy...
--For a similar reason, I like Phanpy better than Donphan.
--I like Poliwag better than its evolutions--it seems so much more innocent and adorable, and I think Poliwrath is just a wannabe hypnotist. Sorry, but Hypno's one of my top ten favorite Pokemon! And Politoed's a wannade Perish Singer--sorry, but Misdreavus is also one of my top ten favorite Pokemon!
--I like Vulpix better than Ninetales! Heh, just kidding--it's the opposite by a landslide.