Bah, MotS didn't screw up anything, it was quite balanced.
For those who say JK/MotS were "unbalanced" I suggest you take a visit to
http://www.jediknight.net/hiss/) if you haven't already. Don't be so hasty...
Certain powers may have been neglected, it's true (Projection for one), but Level 8 Jedi could use all the same powers, so that really wasn't a problem.
In "Personalities" (class based) games, the Scout, Bounty Hunter and Soldier were matched against Level 7 Jedi (no more, no less), so again, it was balanced. The other classes were given varying degrees of weak force, plus "cheap" weapons and armor to make up for their lack of powers, but also had varying speeds and damage ratios.
It was a lot of fun, but some people preferred to have the "Dark/Light" dichotomy. We don't know for sure how the Dark/Light side and its powers will be divided up in JA MP (do we?) we only know that in SP you can choose Dark and Light Side.
From what I hear, this whole notion of using both the darkside and lightside comes primarily from the EU (which isn't surprising, considering how much the DF/JK series has influence and has been influenced by the EU). And logically you could say that powers themselves aren't good or evil, it's how you use them that matters. If you want to play as a "shadow jedi" the closest thing, outside of MotS is probably JK2 SP. ; )
I thought I read somewhere that you could have powers from both sides in Singleplayer, but when you chose sides, powers from the other side suffered a handicap. It's probably just an idea from these forums though.
I did post that idea in the past, but its possible others have thought of it too, I just know I did field such a suggestion long before JK2 was released. The other thing I always longed for was a "Dark Jedi" game. Well, we aren't getting that, but we are getting another "choice" game, the first since JK1, so that's fine by me!