He's back in MoP simply because he must return to set this right -- you will note however the writers have severely downplayed his involvement. He's not leading the rebellion. He's not carving a path of fire and jagged earth up to Garrosh's doorstep... he "lends a hand" on the Echo Isles (we do most of the work) and then, aloud, ponders if he should even be fighting his fellow orcs. Later, he continues to show he is pained by what is happening (Horde versus Horde) and that he is going to Orgrimmar, alone, to parlay with any orcs not currently sipping the Garrosh Flavor-Aid. He's definitely not psyching us up.
In my personal opinion, yes, I think Thrall should be doing all of these things... he should be more active, more fist-pumping, because he is a Horde hero. He should go out with a bang. But the writers again seem to be tucking him into bed. and he's very reluctant right now to make any bold moves to retake the Horde. Maybe that will change in SoO and he'll be there rallying the players and NPCs, but I somehow doubt it. We'll see Mopey Thrall in his robes (not the Doomplate) grumble at Garrosh during the final fight, become disabled, and then we have to clean up. Heck, I wouldn't be very surprised if Thrall handed the Doom-gear down to the next Warchief after SoO -- something that significant would truly send Thrall down Retirement Alley.