I've got
Infinity 5002i 5.25" speakers all around in my '01 Sport and have no issues with the windows rolling down.
Having said that, comparing the 5002i with the
6002i (same thing only in 6"), the 6002i appears to have a mounting depth of 2.25" vs. 2-7/16" for the 5002i - the larger speaker actually requires *less* mounting depth. There's also a
6002si that's the same as the 6002i, only in a shallow-mount (1-7/8" depth) format; this may work for you. It looks like there's no shallow-mount equivalent to the 5002i, FWIW.
One caveat about the 6" speakers: you may have to cut out the existing speaker hole in the door frame to make it fit. I seem to remember trying the 6" units in there and they wouldn't quite fit - so I ended up using the 5.25" ones instead. Installation was pretty easy, but you will need to drill screw holes for them as they won't quite line up with the factory mounting holes.
And yes, I am a big fan of these speakers - I've had the 6002i all around in my car for the last two-plus years, which led me to get the 5002i for the Jeep after I picked it up. Even with them connected to the factory tape player, the sound is great. Can't wait to get a decent head unit in there in the next few months.