My comment was about both the coalition idea and the internal management idea. It suggests that after a certain amount of expansion it would be impossible to expand more without your entire country imploding on you.
As for mechanic's you posted a list of ones that are already in game but other than coalitions didn't list any changes to them. Just that they could be used. That's great but used how? Be specific.
I wouldn't want it to be impossible - I'd want it to be extremely difficult. Look at examples of super blobs in and around the EU4 timeline: the Mongols blobbed across Asia and then broke up into separate and competing factions, the Habsburgs "released vassal" (i.e. their Austrian holidngs, which were governed by a viceroy), Napoleon lost the war to Russia and his empire crumbled. The large empires that did survive (British, French, Spanish, etc) were first of all still relatively evenly matched and second of all were still subject to major setbacks: a number of colonies won independence in the EU time period (USA, Mexico, Haiti, etc). Whereas in my recent playthrough, a two-continent rebellion of 5 colonial nations took me a year and 45K troops to put down (because you can white peace to retain status quo).
There have been a lot of ideas already mentioned in this thread, but some things off the top of my head:
Coalitions need to take into account the balance of power. For example, a blob that matches the 4 biggest powers in its region in terms of military power should make coalitions more likely. The specifics don't have to be exact, but my point is the principle.
For rebels:
- smarter AI movement is a simple change (i.e. not walking into a massive enemy army + running away from superior forces to hide behind a ZoC, etc)
- removing obligatory stackwipes
If the above two are not enough, you could add:
- additional covert support options (think Putin's invasion of Crimea) like sending your own troops if they're separatists from your country or arming them with your weapons (giving them your tech level)
- growth of Zealot rebels over time due to volunteer recruits from neighboring co-religionists
- rebels making use of land they conquer (taxation, trade, recruitment, and manpower)
I have a bunch of ideas for states and cultures, but I think you get the point. Concrete ideas aren't that important at this stage - the point is that the changes could be made if it was so desired.