The 4.6 was prone to intake manifold failure. Not a cheap repair, once labor costs are factored in. Even if you do it yourself, the part alone is quite expensive.
The 5.0 is much easier to work on, parts are cheaper and more widely available, has a better aftermarket for upgrades, etc. Dollar for dollar, I would guess that you could probably tune the 5.0L to produce much more HP than the 4.6, since the 5.0 / 302 was the primary Mustang engine for many years (was replaced by the 4.6 as the V8 Mustang engine in 1996). The 4.6 is relatively new in comparison, and while upgrades are available, they are much pricier than the 5.0 parts, and not as prevalent.