Yeah bro, enlighten me, would be the jesus.
Well first let me start on the intangibility ability. What he is simply doing is simply taking the parts of his body that is getting hit and teleporting the somewhere else. This was noticed by Kakashi during thei first meeting.
Alright now to the MS. Yes it hasn't been confirmed yet. You know how MS has special abilities for different people such as Itachi's genjutsu, Amaterasu and Kakashi'ms Kumai. Those are all techniques regular sharingans are not able to have. To put it simply, Tobi's S/T is one of the most OP abilities and a regular sharingan does not have this ability. Its specific to only him. And don't get confused with Kakashi's and Tobi's ability because they're totally different.
Tobi is also able to control Kurama in a way similar to Madara. We all know a MS is required to control a tailed beast. Madara actually was controlling Kurama with what appeared to be a regular sharingan during his fight with Hashirama. We all know Madara had EMS during tthis time. This lends to the theory that either like Madara, Tobi can use MS abilites while his 3-Tomoe is activated or or well that's about it.
You might ask why he would use his MS ability while his 3-Tomoe his activated. Well its quite simple. Tobi doesn't want ro go blind. He doesn't have any spare MS laying around. If he were to go blind, he'd have to replace it with another 3-Tomoe which probably wouldn't work. Plus he'd lose his S/T technique forever.
Alright one last thing. Tobi controlled Yagura, a perfect Jinchuuriki with a genjutsu so powerful, Mei and Ao thought it was connected to Shisui's genjutsu which is the most powerful genjutsu in existence. We all know genjutsu like that don't come with the regular 3-Tomoe. Especially genjutsu that can control perfect Jinchuriki's. Remember, its just a theory.