UGh, the great chevy vs. ford debate.
First off...I went through this myself recently, and while I am different from you, I'm sure you can learn from my experiences.
Secondly, the reason the F-body died and the mustang lived on has nothing to do with which was the better car, it had to do with branding and marketing, as well as sales of the v6 to, you guessed it, young women (FYI I have no problem with young women at all, they were just not the target market of the F-body, and that is what killed it)
With that said, lets clear up some confusion.
Stock for stock, the Pontiac is the better muscle car. It will outhandle, outbrake, and outaccelerate the Mustang.
However, that is not the extent of a car purchase. The mustang seems to be the "easier" car to drive, and it is. this is because the mustang's upright position and stature are very similar to a "regular" car. The F-Body is long, low, and wide - quite clumsy on first approach. It definetely takes more skill to drive an F-Body fast (around a road course), than a mustang. But, in reality, the F-Body has higher limits.
A problem that plagues all but the highest F-body models is crappy springs/shocks. I drove a trans am back to back with a firehawk, and the difference is night and day - the trans am felt like a fast caprice, the firehawk felt like a sports car. Very different.
The mustang GT, however, from the factory, comes with a "sportier" setup, more in line with, I'd say, a Trans Am WS-6. Comparing base Trans/Firebird to GT, the GT will always seem much better handling.
Engine-wise, I feel there is no comparison. The LT1/LS1 engine makes more power from the get-go, is nearly bulletproof, and can make INSANE power with Head/Cam swaps. The Mustang engine is also a fantastic engine, but I feel the aftermarket hasn't quite caught up, and OHC engines are peakier, heavier, and require alot more parts (2/4 cams versus 1). The best mustang results seem to come with a power adder (SUpercharger/turbo). OF course this is in reference to the modular mustang engines, the 5.0 is a whole different story and benefits from a massive aftermarket and reputation. I prefer the 5.0 to the 4.6.
That said, depending on use, my choice was the Pontiac. For everyday driving I'd probably have chosen the mustang, but as a "project/weekend" car, I wanted to have the most performance money could buy, and for me, that was the Pontiac.
-Tom