Even though (as mentioned above) Nemesis is going no where, it is still a good question as to what Alton will do with where Nemesis currently sits.
I don't think it's really something that needs to be discussed fully just yet. Although Alton will only have a very limited number of choices as to what they can do with the area. They could either build a replica ride of Nemesis (most unlikely), fill in the pit and start fresh with a empty piece of land or attempt to build another ride within the pit (it would be hard as the pit was designed for Nemesis, but there are ways they could get around it).
It'll be interesting to see what will happen to Nemesis, how Alton Towers will go about announcing it's removal, how they will send off the ride that made Alton Towers what it is today and ultimately, it'll be interesting to see how the public would react.
Although hopefully we'll have a ground breaking roller coaster by then that will foreshadow Nemesis, luckily Alton Towers have got a lot of chances to create a coaster that will create the same hype as Nemesis did - lets hope they don't mess it up.
Actually, I'm rather interested in seeing whether the popularity of Nemesis will ever go down hill, are Alton really capable of creating something more special? Time will tell I suppose, but as of now, we do not have to worry about the removal of Nemesis but I must say, it is still an interesting question, what will really happen when the day comes that we have to bid farewell to dear Nemesis?