My Wrangler came with the same Sony Xplod with removable faceplate that q-tec sells. I tried that with several speaker combos. It stunk. I replaced it with a $40 EBay factory CD/cassette stereo for the same reasons as you, but I didn't want amps or subs.
I tried the 5.25 speakers (pioneers) with metal adaptors. They couldn't handle the tiny kick of the factory stereo. My buddy had some kicker 5.25s he let me try out, swapped them in, tried the metal adaptors and plastic adaptors with same result. They rattled and vibrated like crazy, sounded like crap.
I pulled the kickers out and got some 4x6s from Crutchfield (Boston Acoustics, Crutchfield supplied the adaptors for free) and the boom-mat baffles form Amazon for $8. Stuffed some polyfill from an old pillow in behind them and they sound absolutely fanastic.
A lot of guys swear by the kickers and the 5.25s, I didn't have very good results from them. I've ended up with the factory stereo, factory size Rockfords in the sound bar, and the BA 4x6s in the dash, didn't have to cut anything or modify anything, and to me the sound beats the heck out of the Xplod with 5.25s.