I posted this exact question a few weeks back, and I chose to get the '04 Cobra, here's why.

The '05 Mustang has a newly changed up 4.6L engine, new computer system, and a redesigned intake setup. To me this signals a 2-3 year wait in really good performance upgrade availability.

My thoughts are that I can sell the Cobra in 3-4 years for a newer designed SVT Mustang, but in the meantime I can enjoy all the current and available mods for the 99-04 Mustang now, not later.