(Judging these on much more on design and concept rather than battle utility.)
Definitely agree with a lot mentioned above. For me, the most mediocre tend to be the ones that seem completely redundant and pointless. Gen III and especially Gen V had the most of these, IMO - I'd say that had a lot to with how much less previous Gen mons both featured in their main games, so they had to fill a lot of niches that earlier generations had already done.
IMO, the worst offenders are:
The Roggenrolla line: Something about its design just seems so uninspired and unmemorable. Just blue-black rocks in weird shapes, existing for no reason other than the game needing something Geodude-esque to populate caves. (Woobat mostly avoids this, thanks to its typing and interesting design).
Sawk and Throh: They're basically Hitmonlee and Hitmonchan, but instead of the latter's unique designs, we got two Sesame Street characters in karate outfits.
Basculin: I can just imagine how the design meeting for this one went:
"Okay, we need some sort of fish players can catch with the rods, but we can't use any of the roughly two-hundred or so fish pokemon that already exists. How can we make this one fresh and new?"
"What if there are two types, which look slightly different from each other if you look at them really closely?"
"Yeah, that'll do."
Venemoth: Probably wouldn't have considered it if someone hadn't mentioned it up above, but it has always struck me as pretty superfluous when you already have Butterfree and Beedrill. Venonat is fine, but Venemoth is just boring. I tend to forget it even exists.
The Beautifly and Dustox lines: Venemoth may have been a bit redundant, but both of these lines have always seemed utterly pointless to me.
Plusle and Minun: They're Pikachu, but without any of the latter's battle utility, unless you happen to be taking part in one of Ruby and Sapphire's ten or so double battles.
(I had much the same opinion of the Walrein line when I first played Ruby and Sapphire, but the designs have grown on me in the years since, and I actually rather prefer them to the comparatively boring Seal and Dugong)
Alamalora, or however the heck you spell it: Was going to put Luvdisc here first, but, while it is pretty useless, it is at least a fairly unique concept. Alomalora would have been fine were it an evolution of Luvdisc, with some beefed up stats, but as is, its basically just Luvdisc with a slightly different design, and I've never quite been able to fathom why it exists.
Bouffalant: It's Tauros, but with an afro. Okay, then. Again, as an evolution of Tauros, it would have been a worthy addition (though the general concept behind it still baffles me a little.) But as a single stage Pokemon, it just feels like yet another example of B&W filling niches that didn't need to be filled, due to the ban on Pokemon from earlier generations.
I quite like the Bergmite line, actually - something about their designs is really aesthetically appealing, IMO.