Obito, Kakashi & Mangekyou Sharingan
This is a theory a friend of mine came up with a couple days ago so I thought I would post it up to get the opinion of others. Also, I haven't seen anybody come at "how Kakshi obtained MS" from this angle that about to present so hopefully it's fresh and welcomed by all.
Now, we all know that Kakashi got his left eye replaced with Obitio's left eye that was already Sharingan activated. Thus, Kakashi's Sharingan is always "on".
Now, lets assume that Obito didn't die (no proper burial or burial site was ever shown, just his name on the hero stone in Konoha.) It's also possible that Obito could have suffered memory loss. What if Obito obtained the MS during the timeskip. Obito could have made other friends, that became very close to him, after they revived him and nursed him back to good health and somehow, during the timeskip he ended up killing them, whether it be directly or indirectly and with that, even though the other eye wasn't attached to him, it still activated within the other eye that was with Kakashi.
If we go on the "speculation" that Tobi is infact Obito, that would make him the 2nd MS user Itachi talked about, also ruling out the "speculation" that Kakashi is the 2nd MS user and still keep the storyline in tact.