MGE was/is to me the most interesting thing about Morrowind modding. Especially since I can't stand the combat and a lot of game play mechanics. Oblivion has OBGE - much easier to use actually.
To answer your question - first a a question: Do you plan to use a lot of mods?
If no then you will probably be ok with http://www.tesnexus.com/downloads/file.php?id=2097. Get the http://www.tesnexus.com/downloads/file.php?id=32277 for more features/updates.
If yes then you are better installing with the BAIN feature of http://www.tesnexus.com/downloads/file.php?id=22368. For BAIN here is my http://www.gamesas.com/index.php?/topic/1084204-bain-mod-installation-projects/, http://www.tesnexus.com/downloads/file.php?id=35230, http://tesivpositive.animolious.com/ (for all around help). If you are familiar with Wrye Mash then it is not such a large jump. Another factor is are you going to use a bashed patch - many mods require it. If so then Again BAIN. Right up front I'm biased toward BAIN - read my thread for why.
Those are the two main choices. Expects posts to contradict me soon.
Also read the pinned threads above on MOD FAQ and Compatibility and You.