I've contemplated similar, although I have an auto and would rather have a stick. But if I had a stick LS3 SS, the CT4 is not enough to make me want to swap. Much smaller, and with a few bolt ons the SS would be about equally quick. IMO I'd much rather have an LS V8 over the TT6. Sounds better, easier to mod, easier to maintain. Even my SS being a slushbox, I just don't have enough pull towards the CT4 with a stick to seriously consider the swap. The SS is just too damn enjoyable.
Now a CT5 on the other hand, all bets off. That's a nice package. I did see one in transit on a dealer website indicating no markup (who knows if that will hold up) BUT it was an auto. If you can swing a CT5 BW financially (and not pay a 50k markup), then I say pull the trigger. You get the blown V8 and some nice performance goodies plus a few better features on top, and a new warranty. The SS is the last of it's kind for a Chevy, the CT5 same for a Caddy. If these were more traditional times with the car market, and I could get a stick CT5 at a GM employee price, plus 35-40k trade for my SS, I would probably jump.