Leliana is awesome, if you choose her and dont make her a "End Justify the means" person she basically reenacts a less bloody version of what happens to the Catholic faith during renassance.
She allows all races to participate in the Chantry hierarchy, disbands the Circles (and make mages their own police), i would also guess Templars become obsolete then.
Naturally that fractures the chantry beyond hope (alot of people dont like those decisions) and it becomes essentially like protestant christianity, where you have small cults/sects that follow their own splint off view on the Chantry.
Leliana is also awesome enough to allow such cults to establish themselves, essentially ending the Chantry's influence as a political figure.
I actually loved that ending, i just wonder if we will be able to continue from there, i mean the Chantry as a powerful institution doesnt exist anymore in that canon, thats quite a big change.