First off, the indash speakers cannot be replaced with 3.5's. The speaker size is about 2.5 I believe. The mounting depth is not too deep either.
Even if they are good they won't sound good because they shoot straight into the windshield.
I highly disagree with that statement. Glass from your winshield will not absorb sound but reflect the waves towards ear level. If anything it may be too harsh, but that is where crossover levels come into play. Dont worry too much about your rear speakers yet, since your front stage is the most important part of a true soundstage. I would suggest buying a nice set of 6.5 in 2 way components (focal would be a nice choice); stick the midbass in the door with a custom baffel & polyfill, and your tweets in a custom enclosure in the dash location. There is a guy on this forum who actually used the lids from spraypaint cans for his tweets and put that in the dash location for a perfect fit.
Although kickpanels would be ideal, using the method above will save you a bundle$$$.