What I would do is make sectors player-definable again and make a limit similar to fleet-cap that determines how many systems/planets are able to be placed in a single sector.
That would still be problematic, since this would mean that, with low hab-settings there would still be many one planet sectors, and with higher settings, there would be quit a lot of habitable planets in a sector, so I am not sure this would be much of a solution, other than a "cosmetical fix for some ugly sectors".
That said, I don't mind how it works now with the 3 system thing. But it would be nice if you could still create a sector manually from a given system. As it is whether or not a group of planets end up in the same sector depends in part on the order in which you colonise/conquer them which feels wonky to me. It does add another little benefit to habitats, though (using them to determine the origin point for a sector).
It is worse than that. I play with a private mod that makes sectors bigger. It seems, the game is unable to delete sectors that are empty, or shouldn't exist anymore.
If you conquer a colonised system, the game seems to try to let this system stay in the sector it previously was. You can easily see that by playing a Fanatic Purifier and use (or make a mod) with asynchronic sector sizes (6x for core sectors and 4x for frontier sectors) and then go and conquer an empire that is within reach of your core sector (make sure to only land armies, after you conquered all of the outposts). I always try to conquer colonised systems in a certain order, to have a more logic sector layout when I'm playing as a Fanatic Purifier, and I often see that colonised systems are part of sectors they shouldn't be. Only a few weeks ago I conquered a direct neighbor, and all but one system were part of my core sector, only their capital was in its own sector, complety surounded by my core sector. After I reloaded that game the next day, the sector was still there, but had no planet in it, since the system that previously was part of it was now part of my core sector. I also had the phenomenon that a colonised system, that should have been part of an existing sector, was in its own sector, completly destroying the layout I had estimated.