Chances are I'll get bombarded for saying this, but I don't really mind. Pretty much half the cast of R/S/E was a waste of time to train, in my opinion, I didn't think they were near as creative as the others, and they just -felt- weak. It felt like I was playing a bootleg version of G/S/C, I'm not talking down to those of you that like it, more power to you, but I really didn't get that much enjoyment out of it. It didn't strike me as the direction Pokemon should be going in at all, and it seemed like finding anything worthwhile that -looked- decent was a complete hassle. I'm not saying they have to be beauty queens, but I don't want a dancing fat thing with maraka's or a kangaroo with a sumbrero mushroom head.
Like I said, if you like it, more power to you and I'm glad some people do, I just didn't particularly get the same feel from it as others did apparently. Now aside from that generalization that will probably iritate a few people, and I'm sorry for that, I'll name a few off the top of my head.
Wobuffet - Completely worthless outside of competition, and even there its hated.
Ledyba/Ledian ( Spelling? ) - Down right nasty, bad type, bad stats, bad everything.
Onix - If you can't trade, he's dead worthless. He takes a beating from a few of the most common types in the game and has a bad move pool compared to things like Graveler.
Moltres - Unless you teach it Flamethrower, it will basically be a Fearow with boosted stats. Don't even get me started on how it should've had Flamethrower in the original R/B/Y games, because it'll never stop.
Pikachu/Raichu - I only say this, because any sort of physical damage WRECKS him. I had one on my previous FR game, and it was a steady advantage of the Electric type, however, it made me burn up several more items than another more skilled Electric type would, Ampharos being one. Not to mention, you have to coddle it as a Pikachu for awhile to get most of its respectable moves, unless you really feel like blowing money on TM's for a Pokemon that really isn't that great.
Anyways, thats the short list of Pokemon I have/never will train again/ever.