If you have previously installed other anti-malware or anti-virus programs (and I assume have now uninstalled them - if not, that is almost certainly the problem and they should be removed (except for Malwarebytes, Prevx, and most of the anti-spyware only products)), they may not have uninstalled completely or properly unless you used the proper removal tool. These remnants can affect the update and scanning timing of MSE (or any other such program you are using). If this is the case, see the first post in List of anti-malware program cleanup/uninstall tools which lists the removal tool links for many of the most popular products (though you may have to search for yours if you used something not on that list). Run those that are applicable and see if that speeds things up.
I hope this helps.
Good luck!
P.S. I get my MSE updates automatically through Windows Update when I'm essentially not using the system, so I have noticed no problem with the updates. Even when done while working (for whatever reason), they really don't seem to take that long (though they can take up a significant amount of resources when happening).