Some afterthoughts I had after writing that post, and didn't feel like making such a huge edit:
What I think they need to do with the MoP Endgame System:
1). Your Chance for getting a drop in LFR should increase by 30% every time you use a coin, to the point that every 3rd coin you use guarantees a drop. Once you get a drop after using a coin, this counter gets reset. So, on the first boss you use a coin, you have the chance from the boss drop + chance from the coin drop and +30% drop chance ontop of that. Second time you use a coin, you get the chance from the boss's drop, + chance from the coin drop, +60% drop chance. And the Third time you use a coin, you are guaranteed an item from that boss. This would also make coin use more strategic (last boss drops a weapon I need? I better use 2 coins and save the last for him) as well. If you Don't use a coin and get an item, the counter wouldn't be touched at all.
By doing this, you ensure that LFR remains a viable way to gear up (and you don't blow coin after coin after coin and see only 28g pop up in the window).
2). Leave dailies and reps alone (other than the bonus in Patch 5.1), BUT instead, make end-bosses from Heroics and Scenarios drop Rep Gain tokens. Said tokens give +250 rep (maybe 500? not sure) to a faction of your choice. Each Quartermaster would allow you to turn in said token for rep with that faction. That way, if you do lots of Heroics, you can gain rep in some way other than dailies, but yet not gain rep so fast that dailies are no longer necessary (which is how it was during Wrath and Cataclysm; who needs dailies when you get 2k per dungeon run?). Perhaps the Scenario bosses' tokens should only give half rep that the Heroic ones do; Scenarios are much shorter and easier than Heroic dungeons.