Excommunication can be a big problem if you get your zeal up.
Zeal can be your ally aswell. If you play a smaller catholic faction, leave the HRE alone for a century or so until its gobbled up some more territory, then move inquisitors in but keep them moving around so that they only increase zeal instead of burning people, provoke an attack and get them excommunicated. Thier empire will start to crumble as rebels pop up and every catholic faction on their border takes a bite. All you have to do is grab a peice.
It is difficult to get them excommed, Ive only worked this once, as the Spainish and I kept my empire small once Id dealt with the Almohads. doubled its size once id used all the spare crusades I had sitting around on the HRE
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