JP I went thru similar deliberations before upgrading my sound system and this may be of help - I have been progressively upgrading until I was happy with the sound:
Stage 1 Front Speakers
Front speakers - replacement with Infinity Ref 6510CS
Stage 2 Sound proofing treatment in doors
How To Dramatically improve speaker sound quality for £40 (Dynamat)
Stage 3 rear speakers
Rear Speakers - Replacement with Coaxials (3 Door)
Stage 4 Powered Sub
Small Sub Woofer Under Rear Seats. Questions ?
I have done stage 1, 2 and 3 and am now very happy with the results at a fairly low cost (@ £160). Note Stage 3 mainly benefits the rear passengers.
I like to keep the car looking standard / speaker mods very discreet. which Stages 1 to 3 achieve.
Stage 4 - I have not done this to date, as I am already pretty happy with the sound (and also not too confident about pulling the dash apart).
6x9s will be better than an upgrade with the standard speaker size, but as people say you will probably need an amp to drive them. I reckon you will get much better results with a small sub than you will with 6x9s (can you get a refund ?) If you do install the 6x9s a rigid MDF shelf will make a big improvement over mounting in the existing shelf. You may be able to stiffen up the existing shelf with MDF
I am no expert on car audio, but did research my upgrade thorougly before doing the work. I hope this helps with your deliberations.