I've had a 5.0 and currently have an 4.6 so heres my opinion.
The 5.0 is a better motor if you want to mod. like H/C/I and not get reemed in the A$$hole with bills. The 302 is also MUCH easier to work on. It was my first mustang and I don't think the '03 GT will ever be as much fun as the '88 GT just for the fact that I was 16 when I got the '88 and was just so excited to have a fun car.
The 4.6 is in my mind a better motor all around if you are using the car for a daily driver. Not that the '88 GT wasnt a good daily driver, but the 03 is smoother, more comfortable, and a lot better on gas than the 302 was. Only downside to the 4.6 is the amount of money it cost to mod the car, and the fact that I don't trust the internals for a second and I'm saving for a new shortblock at this very moment. Also didn't like the lowend but a set of 3.90s cured that

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If it was up to me I'd have both motors, the 5.0 to mod the hell out of and the 4.6 to just drive around and enjoy myself.