Clarke's update:
Any sufficiently detailed sector control system is indistinguishable from micro hell.
There is a real problem in map terms caused by the lack of 'oceans' in addition to the difficulty gaining access through other countries. In EU4 there is this whole other part of the map that is controlled separately from the large land masses. In Stellaris, as in other 4x space games, space is a series of islands and you have big areas of influence between them.
Fallen Empires should be 'oceans' in more cases, imho.
Militant Isolationists - Unpassable
Keepers of Knowledge - Civilian access
Enigmatic Observers - Military access, can't battle without drawing FE aggro
Holy Guardians - Military access
We're gonna need more of them at that point, though.
That, or turn all blackholes in wormholes for everyone with a mid-game tech.
Imagine if there was a spiral galaxy setup, but there was an "inner ring" that you could access but not colonize or build inside of. You "hop on" then "hop off" at various places along the configuration. Good luck justifying that in the lore, but map wise it would allow for a similar sort of concept, where you could in principle be "land locked" but there were also star systems that had access to this interiour hyperlane network.
Stellaris offering 3 kinds of FTL is an interesting idea, but I would contend probably to its detriment. Not only in the sense that it's challenging to balance well, but also in that kind of throws out a lot of tactical or strategic considerations if you can't be sure of what your enemies are going to have access to. Warp drive is extremely boring, while Wormhole and Hyperdrive both have very interesting properties that impact strategic thinking - you have to defend wormhole stations, and you have chokepoints that you can defend with hyperlanes. I think hyperdrive is probably the best/most interesting from a game design perspective.
A lot of the crappy nature of fighting once you actually get to the gravity well would be fixed if there was a predictable way to tell where people would show up when they dropped out of FTL. You'd need an overhaul for that probably, limiting the number of places FTL travelers could appear to a few per system, perhaps even with fixed exit points when coming from certain directions.
Military stations force FTL exits in their range, though. There's a battleship upgrade that does the same too, i think.
Have you tried your swarm missiles against corvettes which have point defense?
Not throughly.
AI doesn't war metagame, it seems.