Well, it has been awhile since someone's brought this up I suppose...
Why? All he's doing is lifting a guy onto his shoulder and dropping him onto his knee as he raises it up. He isn't throwing them into the air or anything. He hit a pretty sweet looking one against Kane at No Way Out, and against guys like Henry and Show, he can use the Savage Elbow. And then on top of that he has the Anaconda Vise. Besides, a lot of Punk's offense is based on strikes, and dropping someone onto your knee whilst lifting your knee into their skull sounds like a pretty damn nasty strike to me.
Punk's hit a few shite ones in the past (ask Snitsky, Mysterio, Kane just to name a few) but its been a while since I've seen him hit a truly terrible one. Saying that, Punk has really raised his game in the last 12-18 months, and become one of WWE's most consistent in-ring performers; GTS included.
As far as the Pepsi Plunge goes...just no. HHH or no HHH, the WWE wouldn't have someone using a top-rope version of a current superstars finisher. Doesn't matter if its HHH, Cena, Orton, or hell, even the Cobra. Forget about him saying it fucks his knees up; that may be true, but he still wouldn't be able to use it. Superkick? Don't recall ever seeing Punk hit one, but I'm not personally in favor of that. Cutter? See Pepsi Plunge; not happening. All of those have been used in the WWE before, where as the GTS and the Vise haven't. You say them; you think of one man (in WWE terms. Kenta still owns the move) They're synonymous with Punk as far as American wrestling goes.
In all seriousness, the GTS is the move that won Punk the WWECW title, his first WWE title, two of his world titles, and has put away countless opponents. He's used it as his primary finisher since 2007. Be realistic; it's going nowhere.