After three Troopers I'll agree the sound system can be improved. Pretty much you're getting into personal taste territory though. In my '88 LS Trooper I put a good Blaupunkt head unit with the better Blaupunkt speakers (all two-way) and was pretty happy. In both the '95 Limited and '93 RS Troopers I went with Sony ES heads and Polk two-way all 'round and found that an excellent combination. I was particularly impressed with the Sony's tuner which was very sensitive and clear. In all cases the speakers fit the stock locations with no modifications and were well balanced to my tastes. I do like to turn it up from time to time and only occassionally wished for a subwoofer. As a former club DJ my damaged hearing requires a bit more volume than most, so clarity is important.
Currently I'm looking at a Kenwood DVD/Navigation setup as I would like the in-dash video (for eventual rear camera hook-up) and am a current SIRIUS subscriber. Kenwood also has a nice looking composite amp that would handle the stock speaker locations (will go Polk again) and two 8" sealed subs. I'm working on a deck-type enclosure for the subs and amp to fit in the cargo area and look as OEM as possible. The VX doesn't have the room to play like the Troopers, but a good head/speaker combo is an easy afternoon install. Just be sure to get good, quality components and don't skimp. You'll regret it everytime you drive!