My opinion on over-used pokemon:
If you consider using an overused pokemon in your fic, make it your own and try to make it interesting. Give it something truly unique, perhaps it has a negative attitude towards others of its kind, or something.
Having your character own an over-used pokemon and making it nothing special is rather boring, even more boring than an underused pokemon used the same way.
Some ways to spice-up your overused pokemon:
Speech: Everyone needs someone to talk to. However, make it a unique form of talking. Whether it's an annoying accent, or it uses its gift way too much. This is a feature that you also have to customize. Simply having a pokemon speak for the heck of it is also rather boring...
Different color: You can make it a different color, but try to make the difference in color something special and unexpected. Perhaps it hatched that way, or maybe it used to belong to the father/mother of the character, or perhaps it was a prize in a contest, etc...
Means of being acquired: A lot of fics I see involve people getting their pokemon from some Professor Willow, or something...Try to make it a little different, like it was given to him by his father, or something...or, if you do have the Professor give your character the pokemon, make it a better reason than just being friends. Perhaps the Professor is a good-for-nothing who needs someone to help him with his research...
Other unique traits: Perhaps that Machop has blue eyes instead of red (WildFemaleMachoke), Or that Cyndaquil has a scar across its eye. Every human has their own unique features, so why shouldn't pokemon? Not all pokemon should be created equal, so give your overused pokemon a unique feature. Make it suttle, though; don't give that guy's charizard four wings, but maybe give it an extra finger on each hand or foot. (Though a Charizard with four wings would look darn cool...I'll have to remember that...)