First of all props to Blizzard for making an amazing change. Playing since Vanilla, implemention of achievements was an amazing idea, in till i saw that it locked me into that having a main to care about achievements. Thank you very much for this change , this has brought me back for MOP.
One step further that i'd like to propose would be account wide/faction wide reputation. Due to having different mains for each expansion, farming old rep that i have achieved exalted status but don't get the credit due to on another character still makes achievements of reputation sub standard. Like Ghostcrawlers post, Blizzards idea was to make sure the player could choose character A or character B to play and not have and repercussions doing so, this violates that exact thought process.
My second suggestion would be: To make those reputation achievements count character wide. for example, Character A is exalted with 10 factions, Character B is exalted with 6 different factions. the account has 16 factions exalted and they both contribute to a common goal. this currently does not happen and is painful. This is simply rewarding what the player has done in game. It's not giving the player a free pass its giving the player what they deserve.
This is currently not implemented for achievements such as: The diplomat or X number of exalted factions. This idea will not make reputation account but will come to an even ground for those who change characters but want to farm achievements.
I do realise that this is a working process and would offer my idea to the general public to contribute their opinions to hopefully reach a common goal.