Basically, there are three reasons why a stage can be banned:
1. Results in polarization which grossly favors certain characters (waveshines or Marth's fthrow on stages w/ walk offs)
2. Allows exploitative/abusive tactics (circle camping)
3. Directly inhibits play (FoD in doubles, Icicle Mountain, Flatzone)
In regards to the stages you mentioned (DK stages and Mute City) at least one of the above reasons is applicable to them. Both Kongo Jungles have platforms which promotes camping. (This is a pretty famous example on KJ64:
http://www.youtube.com/watch?v=mTNaAUJZz5k&feature=youtu.be) Japes also promotes projectile/platform camping and immensely favors certain characters who can abuse it.
As for Mute City, Mute City is probably the only presently banned stage that comes close to being legal (IMO that is). Granted, it has hazards and stage changes, but both of these are rather predictable and the transformations themselves are relatively balanced (unlike PS transformations which can range from "ok" to "utter cluster ****"). The main aspect in question with regards to Mute City is the main platform. It is small and ledgeless which can drastically favor certain characters.