I'm not looking for some sort of crazy good sound system. I know that the TJ isn't the vehicle for that to begin with. I'm simply looking for something that's a little better than stock, with some nice speakers. It sounds like I'm going to need an aftermarket head unit in any case, so I'll probably just go with that Kenwood one and a set of nice Polk speakers. Are there any better bolt-in options for the factory subwoofer that don't require any modifications?
Swapping that subwoofer makes a huge difference, and personally I would say it is at best a mid-bass, not deep bass else the center console and your stuff inside rattles like a maraca.
I would recommend either the 6.75" or 8". Dremeling 101 is required, but super easy and you will notice a big improvement.
Kicker CompRT shallow mounts are a great option, both 6.75" or 8" sizes, dual voice coils, and come in your choice of 1, 2, 4 and 8 ohms.