I hadn't had time to check or really think these through so apologies in advance for my spelling/grammar.
Generally, I'd like to see a coherent handling of the new focus on the war between the reps and imps. Here are some of my suggestions:
Expansions
Expansions should focus on key/major turning points or events in the War. For example, the Empire mounts a devastating attack on a key planet and the Republic is forced to retreat; or a new super weapon is found and over a few arcs, the Rep must stop the Empire from completing it. We all know the Empire will be defeated eventually so the stories should all build up to that final inevitability.
Note to Devs: Main NPC characters can be bosses and they don't have to die... If Malgus/Jadus is brought back, he/they would make a good enemy for the Reps over and over again. PVE content CAN end in storyline defeat for one side. Old planets can be reused with new zones opened up for 70+ level players especially to reflect the outcome of the latest updates eg a decimated Dromund Kaas area.
Updates - PVP and PVE
While expansions focus on key turning points or events, the regular updates can focus on the in-between battles that take place during the War. New content for PVP and PVE which are in theme would be great. For example, a Battle for [Planet] update can include an update or series of updates focused on the battle to secure the territory. New WZs which tie in with PVE story lines would be great. For example, a strike force (reference to PVE group) is attacking [key rep/imp base/planet killer] (PVE content), so PVP players must engage defenders to secure distract the enemy etc in the WZ (PVP content). Or PVP player must secure some specific data (eg Void Star) and PVE content refers to the data secured being used in the mission. It could also work the other way round. Note: PVP is now cross-faction so we just have to pretend and make do here.
It is up to the Devs to resolve the conflicts in one way or the other. There should be a back and forth in the War after all. It would just be fun to be in actual War again. There was so much potential before the Zakuul expansions.
Conquest
Conquest can also be tied to the whole theme. For example, each week, the top guilds' scores for Imp side and Rep side can be tallied. If the Imps have more points, they "win the conquest of sector". Perhaps bonuses/rewards should be legacy type so that no one faction is locked out of gaining the benefit arising from faction pop imbalance' or alternatively, this can be looked at as similar to the "light vs dark" mechanic except if one faction wins a planet/setor, a group of "rebels" will pop up.
WZ
A PVP "conquest" running in parallel with regular Conquest. Tallying up the WZ specific points in Conquest for all players (guild/no guild) will determine which faction wins. Rewards credits, tokens for new War decorations etc for participants that complete regular WZ conquests - inconsequential to gearing.
PS: No more huttball.