I feel the karma system is stale(sorry)
Agree. It's a start of a reputation system, but small and insufficient for what the users who need it, need it to behave like.
Apart from the applaud and smite, the number of comments and new topic started by that member shall also be counted. I'm not getting it shall be given great importance but shall be counted.
Dunno. Number of posts are counted separately and available for viewing... whether that has much meaning or not. Of course, the obvious issue would be if reputation is or should be indeed dependent on number of posts.
Like or '+1' system for comments and new topics.(shall be counted in karma)
This sounds useful for a reputation system.
Also, karma must also count the response a topic gets. If a members starts a topic and gets a lot of 'likes' and comments, his/her karma must be greater than other.
Dunno.

. Comments... if the topic starts a "war", it is possible to get a lot of comments.

If SMF should have a reputation system (should it really? I wonder if it's best left to extensions), using it for permissions is a different thing though. Depending on the reputation system's criteria, it could be seen as very useful or very unfair and/or impeding more than helping the building of a community. Not sure. A member who doesn't get "likes" (maybe their posts are perfectly okay, but not exactly impressive) wouldn't be able to do things unless they chase "some more likes"...
I don't know if the perspective I'm looking at things is likely or unlikely to happen, but there's something here I have very strong doubts about.
