Good point, I agree with all of them, actually, though I can't say I have a clue what some of the Advance ones are.
Some more overused Pokemon:
Eevee.
Electabuzz.
Sometimes the overuse of Eevees and their evos can drive a reader insane. If you're going to use an Eevee in your fic, make it have a good personality, or something, like in Nikko to Gekko. Also, Electabuzz has been really used a lot in fics, so watch out if you're going to use one!
Some underused ones:
Aipom
Stantler
Wooper
Girafarig
I like these pokes, but they hardly ever get used!