I watched the film again earlier today and was thinking at the end that perhaps the story would be changed so that Gandalf never goes to Isengard to confront Saruman.

There isn't much reason for them to go to Isengard other than to get Merry and Pippin as well as to get the palantir.

What do others think? Is this likely? How will it effect the ROTK story?

I imagine they will. I think that encounter demonstrates how powerful a wizard Gandalf has become after getting thrown around and held prisoner by Saruman in the FOTR.

I sure hope so, because my biggest disappointment was the "Voice Of Saruman" being omitted from TTT. Somehow the "Saruman arc" of the story has to be closed.

Plus, seeing McKellen square off dramatically against Lee will cause me to wet myself.

Yes, the scene will definitely be in ROTK, and will be a great way to kick off film three. I don't know to what extent they'll show the Voice of Saruman, but there's bound to be a scene there, especially since is gone. Besides, Lee said in an online interview that his character will appear in the third film (duh).

They will have a lot of stuff to cram into ROTK. I wonder if that one will be allowed to run longer than 3 hours considering the success of the other two?
I recall reading somewhere that Lee requested

Actually, in an interview linked to in one of the threads in this forum, Elijah Wood says the third films may run as long as 3½ hours.

Good, but do you think audiences will sit still for that long? (I doubt my parents will )
I guess PJ will not have an EE of ROTK and let the theatrical version stand alone.

i have no doubt.

I really don't think they are now ... sometimes I will evil things to happen to the person who decided to have free/cheap popcorn and drink refills.

I find it surprising that PJ didn't have enough faith in viewers to give them the longer EE editions in theaters. The only reason for not doing this is that he felt audiences would feel the film is too long. In my mind you do not change your art for your audience, you hope to change your audience with your art. And after seeing the EE of Fellowship I am a bit ashamed that PJ didn't think that audiences would prefer the longer version.

That's absolutely not true. This is where studio interference comes in. For a theatrical release, three hours is already pushing it in terms of the number of showings that can be squeezed in a single day, but a running time of 3½ hours will, from the studios' point of view, hurt ticket sales too much.

I will be amazed if New Line, even after such a profit margin from the first two films, allows ROTK to exceed 3 hours.

I hope they do.

Lack of intermissions is a definite de-evolution of the modern filmgoing experience, but it's economically considered 'impossible.'