Before the 50th (in the long time ago year of 2005...man it feels like ages since then!) they advertised that Mr. Lincoln would be replaced by the new 50th attraction and it assured guests that he would return after the 50th. Here is a link to a picture (its another micechat post) that states Lincoln was supposed to return.
I believe Disney just did it to appease the die hard fans, all the while never having any intention on bringing him back!
All sorts of talk about what is going to happen to the Opera House. I don't think there is any doubt that Lincoln will be back - the question is in what form (old show, new show, classic show, showcase for Walt Disney's or Disneyland's history). We'll have to wait and see. But long term, I would guess that they will use that space as a Walt Disney or Disneyland museum of sorts and Lincoln will become a part of that experience.
Won't take much to improve upon the lack luster show that was in there just prior to the 50th.