It's a whole different game without Shepard. People like Garrus and Liara have lost someone they relied on. There's no one with the force of personality to force the Krogan and Turians to get along or get the Salarians to give back the female survivor of Maelon's research, no one to stop Cerebus from hijacking the Mars archive. I've been thinking about running a pen-and-paper RPG based around the idea that Shepard gives his/her life to blow up the relay, and now someone (or someones) else has to step up and fill that gap.
Would a group of new eyes have seen a different solution to the Reapers? Was Shepard a little too good at things, and as a result people just kept throwing stuff into Shep's lap instead of trying to fix it themselves? I really think it could be interesting to play around with.
And now, your questions.
Q1: Are the redesigned SM, Scholo, and RFC debuting with 5.0.4 or with Mists?
Q2: Whatever happened to tier 3 gear? I wasn't doing high-end content back then so I never got a chance to get any of it. Why is there a tier 2.5 but not a tier 3 anymore?
Answer 1: I do not know for sure. I know the level 90 heroic versions of SM and Scholo are not likely to show up, but as to whether or not RFC, SM and Scholo get their upgrades before Mists launches, that I cannot say. The patch notes do not mention them.
Answer 2: Tier 3 gear was attainable using tokens that dropped in the original, level 60 40-man version of Naxxramas. Once Naxx was removed from the game with the patch 3.0 update to the world in preparation for Wrath of the Lich King, it was gone, too. With the further update of Light's Hope Chapel in Cataclysm, even if you were holding on to a token, you won't be able to turn it in to most of the people, since many of them were Scarlet Crusade figures who are since dead.