I like your plan a lot.
I really like the miniature underseat sub that comes with the upgraded stereo package, but the speakers suck. I have MB Quart 6.5" components, and 4" rears sitting in my room. They've been there for months and one of these days, I'll get around to installing them.
I've heard that simply upgrading the speakers yields a MASSIVE improvement in sound quality even using the stock Panasonic head unit (which is AWESOME, BTW)!