Thank you for figuring out that Butterfree is not the best pokemon in the game.
I personally don't see the point of training a Butterfree long-term. Its offence stays bad with no decent STAB for a long time (until that really late Silver Wind, and it's weak and obsolete when you do get it). Confusion is nice early on for all those Machops and poisons, but as the rest of your team grows, you'll find that Butterfree only has the powders and everybody else does the attacking better. Wartortle, on the other hand, gets Water Pulse from Misty, has a versatile learnset (mainly from TMs, but he's a great candidate for them) and can solo the game. Can Butterfree solo the game? There you go. Not a fair comparison.
How about Butterfree versus Golbat? Golbat is limited to Wing Attack for a good long while, which, while stronger than Psybeam (90 attack versus 65 attack) has inferior coverage. Statistically, they're both pretty meh. And Butterfree has options that are stronger than Psybeam such as Psychic, Dream Eater, and Shadow Ball, plus all those nifty status moves.