I cannot think of many reasons to steer you away from getting a 6cyl. The main drawback would be if you ever decide to sell; a 6 cyl just won't pull as much cash as a V8 car in my experience. If you can find a true T5 (export car, right?) then that would be cool and probably a different story.
Mine has always been a pleasure to work on because there is so much room under the hood. You don't have to worry about smashing knuckles very often. Ford did well buidling the 6's; mine always starts for me, even if its been sitting for a long time. Just charge up the battery and pump some fuel back in the carb and your good to go. Parts have always been easy to find, but I don't obsess over finding NOS parts for mine. The only headache I had was finding 4 lug baby moons when I beat up a pair in high school...
I love mine, even though it's been a little neglected since I bought the GT/CS. Driving has always been fun, especially having the manual and 4:10's in the back. Once I transition out of the service and settle down I plan to start giving it some love again, starting with a new clutch.
I'm sure of couple other guys here on the site will have a few things to add about the 6s as well.