I've been using ISE 11.1 for a couple months now and I must say that it makes me cringe when I think about the code that created this monster.
The good - Everything done outside of ISE. I have noticed that the tools which are the backend of ISE and everything they do are very reliable. At least from all of my experience. I'm guessing this is because they are pretty simple single threaded programs who know how to do the work they were built to do.
The bad - ISE. I am very sympathetic to the pains of writing a GUI which has to synchronize all sorts of other tasks. I know this is a very difficult task. You never know when the user will click something or when he might stop a process. ISE has to keep track of temporary files, source file changes, statuses and lots of other things. It's clear that the job is not easy. On the other hand Xilinx is a huge company and has the resources and responsibility to provide its users with a much better product.
In my experience ISE has many stability issues and quirks. I have learned to take them in stride. What I find shocking is that these bugs come from a very bad low-level infrastructure in the program, and not just a random assortment of small mistakes. (This is a huge assumption, but it is based both on my extensive experience with software and multithreaded applications, and on my experience with ISE.)
Example: When you change your source files in an external editor you see that ISE processes those changes only once you change focus back to ISE. Why??? That must be the strangest thing ever. It can actually take ISE seconds (why so long???) before it updates it's statuses - and you can see that in the ISE Processes window. If you click Generate Bitstream, or Synthesize before it has processed and updates its status then it will be ignored ostensibly because the files are up-to-date. This strikes me as an extraordinarily bad way to update internal ISE project status. Once a file is changed ISE should immediately process that and mark that file and all subsequent files as out-of-date.
Hoping for better with ISE 11.2 but seriously doubting it