I own both as well. I can't really compare them though because i hav a modded 5.0 (engine, suspension, braking, etc) and i'm comparing it against a stock 99+ GT. My particular 5.0 beats my GT in acceleration, braking and handling.
SO i'll just offer my opinion on both motors.
5.0
Tons of low end power. Even when stock it would plant you in the seat at 1500-2000RPM. It's always tricky to launch the car with so much low end grunt and a lighter rear. This light rear end also makes it scary to give it gas around a corner. You gotta learn to back off the throttle in the turns because the rear will step out on you. Stock 5.0's suck up top, but some better breathing heads and a cam can fix that. Dollar for Dollar, parts for 5.0's are dirt cheap.
4.6L
Very smoother refinied modern motor. Love the sound. It sounds newer than the gurgling 5.0. Doesn't have that much low end grunt. Launching is a bit easier and the added weight over the rear gives the car a far more planted feel. I can be in a turn and give it full thottle and the car will stay glued to the road. Handles well but you can feel the added weight over the Fox. Over 3000RPM the motor pulls hard. My only gripe is the lack of low end power. I like to cruise around town at 2000RPM. In my 5.0, that was right where all the torque was, so if i needed to accelerate to merge, i could roll on the gas halfway and still take off like a mofo. With the 4.6L, 2000RPM just doesn't have that much power. I floor it and i still worry if i will make it in time. I really need to downshift the car in this situation which annoys me. I'm used to having power in every gear at every RPM. Not so with the 4.6L. You really need to keep the revs up. Not a problem though, i just need to learn this.
All and all, i love both car/motors. I choose to keep my '03 stock simply because i need a commuter car with A/C, that rode nice and was peppy. I don't want to go too crazy with mods. With my 5.0, it's old, parts are cheap, and it's already got a solid mod platform to build on. A few guys have told me to put gears, long tubes, mid-pipe and cat-back on my 4.6L, but right there is half of what i need for a supercharger for my 5.0 which already has those things.