Big things are coming. SCT and SCTD are being completely rewritten from the ground up. They will not only perform better, but give you many more ways to customize your display. New events, multiple display areas to assign events too, and more. Expect a release sometime around the release of WoW 1.12.
Speaking of, no SCT is not going way even though WoW will have its own version of SCT. You'll quickly find it doesn't provide you with many options and is not very customizable at all. I'm more converned about people thinking problems they have with WoW's SCT are connected to the real SCT =)
It still amazes me how many people don't take the time to customize SCT to their liking...you don't even have to touch the sct_event_config file to drastically change how SCT behaves. I encourage everyone to play around, even more so when 5.0 comes out. And what you cannot figure out, ask on the forums or post as a feature!