When I've upgraded my copy of Movable Type to the version 5.2 a couple of months ago, I remember I had to say thanks publicly to Mihai Bocsaru of Pro IT Service for the fundamental help he gave to me: without him, I wouldn't probably upgrade no copy of MT, as several problems affected the upgrading process. That's time to do it.
In fact, there're many aspects to consider when upgrading MT, and several scripts to change and upgrade, in several parts. Without an expert mind, I think nobody could point out all these aspect particularly because they can vary from platform to platform, and from situation to situation ─ depending from your installation configuration.
One point from which start is surely forums.movabletype.org. Here you can find solutions from the persone doing Movable Type, that's clearly the best solution.
In particular, I must thank Mihai for the Signing in stuck problem in comments (consult this post to have information on the whole problem and the related aspects): It was very hard to resolve this also because it was involving several other upgrades to do. But at least all went well.
Another problem you would encounter when upgrading is the inability to properly use the edit window under Firefox 16 or higher. Also for this problem there's a solution, and in this case it's the MT staff developer Takeshi Nick Osanai to furnish it: check the page named "Patch file for Firefox 16 users" to resolve the issue.
Happy Movable-typing!