There needs to be more coercion and military violence involved for these HRE unification reforms. Anything else is simply not realistic.
Historically, attempts by the emperor to establish hegemony were resisted and ended up in the 30 years war, which halved or thirded the population of Germany. That's quite a bit different from how it works un EU3 HTTT, actually it's currently better modelled in EU3 IN, where the way to gain control (and with no permanency assured, that's also a big point) is force-vassalising the electors.