I think each engine has it's pros and cons.
Regular maintenance I'd take the 4.6 any day. Easy as H to change the spark plugs, plug wires, coil packs, serpentine belt, etc...
As for mods, the 5.0's are easier to mod and have more parts available (only 1 aftermarket cylinder head available at this time for the 4.6). For example, I'd never want to try and install headers on my 4.6, a cylinder head swap is also more involved because of the timing chains, etc...
Overall, however, you can't beat the driveability of the 4.6 modulars. They idle smooth as butta, are easier on gas, and if maintained right will run well over 200K miles and not leak one drip of oil. With full bolt on's and a nice set of cams, a 5-speed PI 4.6 will be very close to 300 RWHP.
Another thing to consider is torque. Get the 5.0 if you like the low down grunt. Get the 4.6 if you like to wind it out.