When you say 12" upgrade you're talking the 2-piston F-body kit, right? I've been thinking about both options and the reason I'm leaning towards the '04-'08 is that it's closer to stock and bolts right up like the original brakes, not to mention the lower price point. I'm hesitant to move too far from OEM standards at this early time in my modding life.
What I think I will do is put in the extended front brake lines now, though, so they'll be present if I decide to do the larger setup in the future. My goal at this point is "better", not necessarily "best".
Of course I've not yet bought any parts, and if the F-body kit is really that much better I'm still willing to go that way. Is the setup tricky at all or does it largely just bolt right up? (How hard is adapting the caliper bracket, getting the offset right, etc.?)