well first of all if you decide to get a 4.6l, make sure its a 99+ or if its a 96-98 it has the pi head/cam/intake swap. the 99-mid 01's have the t-45 tranny, while the mid 01's and up have the stronger t-3650 with the infamous 1-2, 2-3 grind/notchiness. 96-98gt's make around (correct me if im wrong) 215hp? while 99+ are 260hp/300ft/lbs at the crank i think.
anyway, its up to you. sometimes i wish i would have a 5.0, but i like the 4.6 too. the aftermarket has embraced the 4.6. it depends on how much modding you plan on doing. if its just basic bolt-ons, the 4.6 isnt really hard to work on. but when it comes to headswaps and cams and intakes, there arent as many options. pretty much vt or comp cams, and ported stock heads, then theres accufab, c&l, dragon intake plenums. you can still make gobs of power with a mod motor. they love being blown

the mods love to rev too. they're also pretty reliable.
with the 5.0, there are a lot more options when it comes to heads, upper/lower intakes, probably more options when it comes to cams too. as far as different manufacturers anyway.
im no expert by any means, but like any car, if you want the power, you gotta be willing to spend the $$$. just do some research before you make you choice. ive had mine for 8 months and im still learning more crap about it every day.