Since 2.2 I mostly play with vassals instead of conquering, because I feel tired by having so many planets in my ledger. I too would like to have the old sector system back.
A good system, at least story wise, could be one in which :
- Sectors are created automatically as administrative units. You can initially tax them as you wish, hampering or helping their development
- You could tinker with those administrative units using unity (or influence, but I think unity is more suited for that)
- Overtime, sectors could develop some personality, appointing their own governors (saving you the trouble to do so), asking for more autonomy...
- You could allow them gradually to have a greater share of their ressources, build their own civilian, then military ships
- At some point (probably when they have their own fleet and want to do their own commercial deals), they could ask to become vassals.
- So ultimately they could challenge you to become independant, if you let them go all the way to this and are weak enough for them to revolt.
However, I must stress that playing a gigantic united empire should still be possible. Forcing the release of sectors as autonomous units could be linked to some kind of liberation CBs. It shouldn't be a natural process that every empire goes to.