It sounds like the best thing to do (without showing a brand bias)
1. Replace the front two door speakers with high quality components (they're 6.5's I assume?)
2. Buy a clean aftermarket Amp for those 2 speakers, depending on the speaker's reccomend RMS power and sensitivity anything from 50-125x2 AMP will be fine
3. Most likely also will need a signal processor to clean up the signal.
Should be around $500-$800 and the clarity will be MUCH better. Then add a sub/amp later if there isn't enough bass but with the newfound clarity and rear fill of the 6x9's you'll probably be happy unless you're a bass-head