My guess is that when trimming down the skill list, Bethesda wanted to drop a magic skill to keep them from outnumbering skills of other types, and they chose mysticism, not sure why, but it might be because all the spells under it could be moved into other schools, which I suspect they'll do, at the very least, since they're bringing back the enchant skill, I'm sure soul trap will stay in the game. Besides, the other schools tended to have a consistent theme to them, conjuration was, as its name implied, mostly summoning spells, destruction, logically, covered spells that cause direct damage to enemies or their attributes, restoration has, well, spells that restore things, I'd consider fortify attribute spells falling under it a bit of a stretch since they don't actually restore or heal your body, but I guess having it only cover spells that do that might have seemed a little too limiting, and so on. But mysticism seems to be where Bethesda throws whatever spell they didn't put somewhere else, so if one magic skill had to get the ax, mysticism seems as good as any to me, as long as former mysticism spells get moved to other categories where they'd make sense. Now, I'm not saying reducing the amount of skills again was necessarily a good idea, but I don't actually believe that a shorter skill list is automatically a bad thing either, unlike some here seem to believe, but the decision to reduce the skill list COULD prove detrimental to the game, depending on many factors such as how it effects the overall game experience, what skills, exactly, were removed, whether this has reduced the player's options, and so on. But since Bethesda obviously decided that they wanted less skills in Skyrim, and they presumably felt one magic skill needed to go, I'd say mysticism was probably the best choice.
the most interesting and mysterious of the magic branches, i assume it was removed to "simplify" magic and make it "less complicated"
Maybe if you define "Interesting" and "mysterious" as "random", because the only thing really mysterious about mysticism is the logic behind the decision that spells that let you trap souls, dispel magic effects, and move objects remotely should all fall into the same school.
Now maybe I would miss it if it was actually as interesting as the lore makes it out to be. But apparently, in game terms, "The most mysterous branch of magic" translates to "A dump for whatever spells we didn't want to put somewhere else."