When I build my stereo system, I plan on using 2) 3.5" midrange drivers in the center dash, 2) surface mount tweeters in the upper corners of the windshield, 2) 6x9"s in rear with directional tweeters that can be adjusted to increase stereo separation. I will probably go without the sub until I listen to the system first to see if it's necessary.
For me, it's all about maximizing stereo separation and clarity while maintaining a stock look. But it's a compromise either way because IMHO, there is no room for a quality speaker in the kick panels with a large magnet, especially the drivers side with the e brake. Even if you did get em in there, that's really not the best position for sound quality. I suppose mounting the midrange drivers in the doors and the tweeters in the upper windshield corners might be sonically better, but again,the drivers side speaker will be a foot or more below your ear and might be where your knee rests. Besides, there are fitment and aesthetic compromises there as well, as noted above, not to mention hacking a perfectly good set of door panels.
This is the setup I plan on going with (and just disconnect the tweeters on the 3.5"), but I haven't checked fitment yet, as this will be sometime this coming year for me.
http://www.crutchfield.com/p_108R3002CX/Infinity-Reference-X-REF-3002cfx.html?tp=96#details-tab
http://www.crutchfield.com/p_108K1011T/Infinity-Kappa-10-11t.html?tp=107
http://www.crutchfield.com/p_091690CA1S/Focal-Access-690CA1-SG.html?tp=91