Our car has openings for 6x9 speakers in the rear deck (also, 6.5" in doors with 1" tweeters in dash). I am also currently upgrading my sound system since the base factory one sucks the big one. I chose the Infinity Kappa series coaxial 692.9i(also available in 3-way); i had them in my previous car and loved them (then they were the 4" though, ugh).
Other good brands to look for are: Focal, Polk Audio, JBL, ect. Best advise is go listen to some at a shop and choose what sounds best to you (just buy them on ebay, it's much cheaper!) Good hunting, and let us know how it turns out.
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