Kamui has three more counters. Things that spawn onto Obito does not activate a phasing ability, such as amaterasu. Any Genjutsu that requires looking at someone can also be used against Obito's kamui eyes, that's just a weakness of having eyes at all though. Though Obito seems strong with genjutsu, I don't think he would be able to break Itachi's tsukyomi though since Kakashi was equal with Obito in genjutsu and we all know what Itachi did to Kakashi. Another counter is that he becomes tangible when absorbing something, something that could possibly be remedied by having both eyes though. Absorb with left, phase with right (if that is possible, which it likely is).
Obito's time limit that he can keep himself phased is 5 minutes at a time, which is also a weakness. I don't know the amount of time he can't phase after that but I assume he just needs to fully solidify and the time is reset. But if someone can keep constant attacks through him for 5 minutes that is a weakness.