I went the reversed route by upgrading my deck first and then upgrading my speakers. But I can tell you that the stock PT speakers are very decent, but are limited by the functionality and sound quality of the stock stereo. You may want to consider adding an aftermarket stereo first, as most often this will fulfill your need for better sound quality, and it's also a hell of a lot easier to do.
Just my 2 cents.
If you have any other questions, feel free to ask.