What you are asking is not really possible to tell IMO. Because there isnt any ONE 'mission-critical' problem with SE5 that I can see. If there were, that would make it much easier to correct.
The 'problem' with SE5 IMO is a combination of subtle things, many of which are touched on above. I am the one in my gaming group that decided to buy and try SE5 despite the poor reviews and less than glowing feedback from many SE4 fanatics. And when my friends ask me about it, I still cant put my finger directly on it.
The end result is that SE5 just doesnt seem 'fun' IMO. And that is about as subjective as you can get!
Whether its the UI or bugs or unfinished features or poor AI or whatever I dont know...but the result is the same...I start a game, play for 15-20 turns, lose interest, save the game, and then not bother with it for a few weeks when I repeat the process again.
So, if you want to sum it up in one problem, I guess that would be it..."IMO, SE5 isnt fun at the moment".