Draztal posted some clarification of the faction/reputation changes happening in patch 5.2, and how the work orders interact with them. A lot of people are at least somewhat pleased with these changes, since they're giving players a slow and steady non-daily quest
way to earn rep.
The main points:
Each day, you earn 750 reputation with the first heroic, and 325 reputation with the first scenario.
There will be no valor rewards for the new dailies faction, only the raid faction.
Shado-Pan Assult reputation can be earned through Raid Finder, but after a certain point only boss kills reward faction rep.
Work Orders require you to be exalted with The Tillers and to have unlocked all plots.
Work Orders will be available for most 5.0/5.1 factions, but will not include the Black Prince.
It's necessary to repeat the mantra that these are all changes being done on the PTR and they could change. Now I personally wouldn't count on these modifications changing too much, they seem to be very fleshed out at this point, but still, anything's possible.
Draztal's full post after the break.
Currently, the reputation for your first heroic is 750 and 325 for your first scenario. The new dailies faction doesn't have any valor items. The developers don't want fresh 90s to skip previous content and jump into the newest, so you'll still need 480 item level, but all the changes introduced to previous content will definitely help catch up quicker (lower prices, higher drop chance...)
Also, the valor reputation can be earned through the Raid Finder too but you need to kill bosses to get beyond a certain threshold. So we probably won't see something like the old Icecrown Citadel reputation runs.
In order to use the Work Orders in Sunsong Ranch, you need to be exalted with The Tiillers and all plots unlocked, but it's not required to own Sunsong. Work orders will be available for most 5.0/5.1 factions, but it will most likely not include Black Prince.