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I've done a few teams in which I have had the same problem.
The last few have been:
Tentacruel
Gyarados
Wailord
Walrein
Wailord had surprised me, but there are no really great options. Shell Bell Wailord is really good for ingame.
I'm not going to lie, I have only ever used Totodile twice in my Gen 2 gaming.
My vote goes to Mudkip because Gen 3 4 lyfe :P
I don't have a lot of Gen 4 Experience either
My choice would have to be Venomoth, it has always been a favorite of mine since I was little. I would always have a lot of problems training Venonat's though.
I did a Mono-Poison run in Pokemon Firered, and my Beedril (named Anthrax) sucks horrendously. Beedril is just to bad to be useful.
Also, a lot of people, barring myself, do not like the actual animals: Honey Bees or Hornets.