SublimeLinter uses a queue, sublimelint uses a single thread runner.
I would like to see some metrics on this. I did some testing and could not detect any difference is speed. If there are speed issues we would like to know.
SublimeLinter is turned on via a user setting. You just have to change the setting once to have SublimeLinter always on.
It can be disabled, along with any of the checkers. I think in the current version or an upcoming version it will be off by default. You can also disable particular pep8 error messages.
In general SublimeLinter is much more configurable. If anyone is having issues with it, please file an issue in the github issue tracker and we will fix it.