If you are concerned about changing the v6 into something of a monster for it's size, then i'd save up for a turbo instead of a trade-in or an engine swap. The depreciation on our car isn't too bad considering others', but it's still there. If you trade in your 2006, you are going to be losing alot more money... ALOT MORE.
Save up and get a kick ass turbo w/ all the works for it (the whole breathing system) and then invest in a take off 8.8 rear with gears. It would probably be insane just from that alone. There's a ton of things you could do to a v6 to muscle it past a GT. The GT is the better power starting point of course. I'd definately just supe up my v6 and make it a pretty mean DD monster.
Power to ya if you go ahead and drop in a GT engine as well... Alternatively you could look at dropping in one of ford's crate'd engines lmao. That might even be easier than the GT engine... You'd also have the benefit of having a great base to work off of, tons of already proven powerhouse mods for the engine, the sound, the option to make it a horrific monster of a sleeper. There are more things needed before you'd even drop that baby in though that you would need to do, but it has been done (to a v6 2005+ mustang).
Just recently (about a week ago or so) I saw this clip on youtube of what i'm talking about.
Although this guy stuck in a FR 460...
Realistically speaking with a budget in mind, i'd opt. for going with a tubo hands down.