Clearly everything points to Tobi being Obito, but I find there are just too many problems with this.
This post will be about why he shouldn't be obito.

First off there is a clear problem with obito being alive at all.
Yes perhaps he activated MS as he was dying, but he was still clearly crushed beforehand.
Now there is obviously something strange with tobi's body, so if they are one and the same we need a good explanation on how obito survived his injuries long enough to transition it into tobi's body; right now that shit is literally magic, unless you want to accept that some crippled near death teenager somehow crawled into oro's lair and injected himself with a syringe of that sweet senju juice.

Second, there is a huge, heck, gigantic problem with obito's death itself.
After minato roflstomped kakashi's assailants, does anyone believe they wouldn't recover the body?
In fact minato could've easily done this himself by just teleporting the rocks away, or just smashing them with his rasengan, or summon a toad etc..
And if he did do that, why would he hide that the body allegedly disappeared? Anything that happened here to circumvent this from happening is either insanely shitty writing or some deus ex machina that prevented minato from recovering the body at any timeframe.

Thirdly, obito and kakashi parted on strong bonds and unless something happened that turned him incredibly insane, which should be something substantial, I doubt rin's off-screen death would've caused him to want to murder the entire village of konoha twice.
Also, even if Rin was the cause of his insanity/hatred, she clearly didn't die right after obito, why the fuck would he hide that he survived? And if someone was nursing him in a comatose state or whatever, that brings us right back at point one.

Fourthly, controlling the kyuubi is more than just having sharingan, hashirama used some crazy sealing stuff to just unbind kyuubi from madara. If it was that easy, kakashi (or anyone with sharingan) should be able to do it too.

Fifthly, the oh so discussed power difference.
The argument I heard here over and over is: "oh tobi is just phasing out it's no biggie".
Problem with this stems all the way back to sasuke vs lee; even though sasuke could perfectly see lee, his body could not keep up at all.
Tobi kept up with minato, a genius hokage level ninja, whilst obito was nothing compared to kakashi; kakashi in turn could not keep up with minato.
Then there is all the prep to get the kyuubi etc..; all of this points to someone who had a lot of time.

This point however could be adressed if the kamui dimension does indeed have a different passage of time

Oh and extensiveuseofmangekyoumakesyoublindetc..