My skyrim via MO2 starting up slower tooCan't answer for that dude and will answer for myself: I don't like the idea of running everything through MO (the game, bodyslide, CK, xEdit, etc). I don't see it as a convenience. Also, launching the game via MO is slower than the standard method (yes, yes, I'm happy for you who have powerful pc's and don't feel the difference). The only advantage of MO that I see is that the mods are in separate folders and easy to delete, but the disadvantages outweigh this advantage (personally for me)
And I have now, if I remember correctly, about 1400+ mods in the build I'd go crazy fixing bugs or reinstalling mods by simply copying them into the Data folder