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I think Butterfree is better overall. It learns a couple of useful status-hindering attacks and learns a few Psychic-type attacks like Psybeam and Confusion.
I prefer beedrill, he looks all mean =] Both are pretty dire competetively so I won't choose on that basis.
FYI, butterfree is no tougher than beedrill. Butterfree has 10 more base defence while beedril has 5 more base HP, boosting his general survivability. Also why is he more difficult to evolve, when poisin has better coverage in early-game (Aka brock doesn't lol at poisin sting)?
For all the above reasons, plus it's perdier and is more useful when battling Brock and Team Rocket. But I've never had a use for it after the second badge in most games.
I prefer Butterfree, as I've always thought of it as a cool Pokemon. And now, I even use him frequently enough in competitive battles. I love pwning people with my Butterfree-not as much as I like pwning with Pachirisu or Luvdisc, mind you, but it's noteworthy nonetheless! :P
I don't really care for either of those two pokemon but if I had to choose one of them, I would pick Butterfree. I liked Butterfree because it was useful to me early in the game in RBY, especially in Yellow version. Even though it is a pain to level up, learning Confusion upon evolving was really useful for defeating Brock's Pokemon and having a Psychic move very early in the game was a nice bonus for all those annoying Poison Pokemon later on.
Though Butterfree is quite beautiful, I prefer Beedrill. Beedrill has a cool and tougher-looking appearance. I also like Weedle and Kakuna more than I like Caterpie and Metapod.
Beedrill, though I know I'm in the minority. Especially in FRLG, its twin needle pwns Sabrina. You can also breed Swords Dance into it so you can really build up a killing machine. True, butterfree gets psychic attacks, but lets face it - a fight between a butterfly and a bee. Who's going to win?