I wouldn't bother tricking the C6... they can handle the power without mods.
Tricking the C4 may actually make it suck less power... I don't know as I'm not a transmission guy.
Trick bits are definitely more widely available for the C4.
If I had no box in my possession, I think it would be a no brainer, but seeing as I already have the C6, I have to take that into account too.
And yes, the C6 is definitely longer, but I think the crossmembers to suit the T5 should work for the C6. The other thing is having a longer speedo drive made up and shortening the tail shaft. Mine was running already though, so I'm assuming the tailshaft is already the right length.