My thoughts on:
Magnemite vs. Klink: Now that I think about it, they are pretty similar. But they're different enough to be fine with me.
Sawk and Throh vs. Hitmonchan and Hitmonlee (and Hitmontop?): These I have a problem with. I could have done without Sawk and Throh being introduced; not only do they seem too similar to Hitmonchan and Hitmonlee, they're too humanoid to me.
Pidgey vs. Starly vs. Pidove vs. Fletchling: Admittedly, they are all pretty similar, but I'm fine with it. They're all based on different kinds of birds (though I'm not sure what Pidgey is; it seems to be a sparrow or something, but its name suggests it's a pigeon), so it's alright with me.
Ratatta vs. Sentret vs. Zigzagoon vs. Bidoof: I don't even see many similarities with these, aside from their place in the game.
Corphish vs. Krabby: Corphish is a crawdad, Krabby is a crab. They're pretty different.
Luvdisc vs. Alomomola: I'm not entirely sure why they didn't make Alomomola an evolution of Luvdisc. Would it be possible for them to make this happen in the next game?
But here's a couple that I don't think have been mentioned yet:
Glameow vs. Purrloin: Evolutions aside, the only difference between these two is that Purrloin is just a darker version of Glameow.
Corphish vs. Clauncher (?): These two seem pretty similar to me, but I don't know much about Clauncher yet, so I'm not sure about this one.