I apologize in advance if these issues are already met in the upcoming 5.3 update. But here are some issues I have found with the current HRE.
Issue 1) Uber emperor bonuses.
Currently the HRE emperor, without including any of the reform bonuses or just being emperor bonuses gains certain benefits based upon the number of states in the empire.
Monthly Stability investments = the amount of states you have in the empire. With 79 states in the empire that means you have a bonus 79 to stability investments. That's pretty OP.
Manpower increase 5X. So with 79 states, im gaining close to 400,000 manpower. Probably needs to be toned down by half or a quarter.
Land Force Limits 2X. SO my 8 province brandenburg instead of fielding 20 units max can field 180. Probably should half this number.
Prestige .1X. So 7.9 prestige per year. That should probably half'd or quartered.
Issue 2) Too Easy to Pass reforms
Because of a weak reformation and a lot of small nations, reforms are too easy to pass. (Small nations and same religious nations are typically auto yes) I'd suggest moving the imperial authority required to pass a decision to 75 or simply editing the modifiers so that the AI dont auto yes. I realize that when De Gratia is working this might be fixed slightly.
Issue 3) Status Quo
If you play a Vanilla DW, you typically see the HRE, while still retain a few small states, usually get split up between a few big players. Usually Prussia/The Hansa/Austria/Switzerland for me. In MEIOU this does not happen and it's normally just staus quo.
The reason for this, is the removal of random cores. The AI jump on cores they gain on other provinces through boundary dispute or claims, and will expand that way. There were also a few conquest to insta core missions that were removed, that did not solve the problem.
I propose that random cores be put back in for the HRE. You could make them AI only too, if you wanted to leave in the challenge of expanding in the HRE for the human player. I'm not sure if the diplomatic hotfix mission is putting the AI against eachother and leading to expansion, I haven't tried it.
You may also want to set the AI up to be aggressive.