If they don't resolve the Mage templar war soon, it will naturally be marginalized to the point of having no true significance. Neither the mages nor the Templars have the resources or manpower for a long drawn out conflict. Some of ya'll may disagree, but considering the templars forswear any outside possessions or inheritances when they join the order (Evangeline in Asunder mentions this) it isn't like they have outside sources of funding to depend on and from the plan Lambert had to start off, it appeared they were going straight at the mages and weren't worrying about setting up any systems of any kind for sustaining the order.
The mages are in the exact same boat, except at least early on they will be much more of a fugitive role then the Templars will, so it isn't like people are going to be lining up to do business with them.
Add in to this that the Chantry is going to be rebuilding their forces, I don't see how the mage templar conflict can at all be meaningful without resolving it soon. If it desolves into this long running conflict between the two groups then it will marginalize into basically side quest similar to the the mage underground and the mercenary group from DAO.
I think it will be resolved, I don't see it being resolved for either a return to status quo nor outright freedom for the mages. It will be degrees between those two depending on what the player does, but unless bioware outright shocks me, I can't see them allowing an ending that grants the mages outright freedom nor and ending that causes a full return to status quo. Especially with their concerns about continuity of player choices. There is literally no way for say MWZ and Xil to have compatible games if you give that wide of a berth of endings and don't do something along the lines of "Well thats what happened, but then this event occurred and completely changed everything to this" which basically removes any importance of actually allowing the differences in the first place.
Oh, and Uldred had been planning his move for months in advance if you read Irvings writtings, it wasn't circle autonomy, it was a power play by Uldred. He wanted to call the shots.