Doomdark has said elsewhere that elective feudal monarchies will have some interesting rules in place to make the succession an actual election, and not just a "most titles win" mechanic like elective law in CK1.
This single revelation tells me that the HRE will get some love, even if there are no other changes. An elective law like the one he describes in the other thread (I'm lazy and don't feel like linking at the moment) would allow for internal bickering over succession and actual "elections" with the powerful magnates of the realm supporting candidates. This would give us a mechanic for the HRE at some points of its existence by default, without even factoring in empire specific game mechanics.
While I have no real concern with the number of tiers in the game, I do hope that CK: DV's mechanic for the Pope giving the imperial crown to powerful secular rulers (regardless of HRE affiliation) is still in CK2 in some form.
While the HRE is important, I feel that opening the game up to allow for other possible emperors is important, as the HRE and Byzantium can both be wiped out in-game. Any Catholic ruler with enough political clout should be able to become an emperor... if the Pope wants to cooperate.