I think Klink family is unnecessary, we already got Magnamite family, which is good enough for me.
I don't have a problem with Pidgey (my second favorite family), Hoothoot, Taillow or Starly, because they're a sure member on my team in each of those gens. I don't like Pidove's family design, but there is no much similarity on the birds.
Sawk and Throh should'nt even exist...
Tauros and Bouffalant do look alike... of course Tauros is better.
I'm fine with the first 3 generations rodents, I think they are based on different real-life rodents and don't have much in comon, but Bidoof and Patrat do look alike to much.
Now the bugs... Well a lot real bugs are worms which go through a metamorfosis and become something else, so there is no problem for me. But Beautifly's design is similar to Butterfree, (maybe they wanted to make a cute butterfly) still Butterfree is the best one.
I agree with the other ideas mentioned. Maybe pokémon look like others of different species in the same way that real animals does, maybe because they have a common ancestor?... (I've always think of Kabutops being ancestor to Scyther and Aerodactyl to Charizard)
Well that' just my oppinion anyway.