IMO one of the main issues of CK2's empires is simply that de jure empires functions exactly like de jure kingdoms.
De jure kingdoms mostly work (atleast in western europe) by keeping the kingdoms together, maybe expanding a little, which isn't that bad. But it completely breaks on empire level, simply because they're so large, while none of the de jure vassals wants independence, which is in no way realistic.
the HRE is probably the worst example of this - it was, with a few exceptions, not really capable of projecting the kind military might it can just endlessly do in CK2.
Something I've been thinking about was that the further away a war is from the main holding of a vassal, fewer froops are provided by said vassal..