As a whole I completely agree. The only thing that annoys me is there being no counter to choke point defense. This is hardly a problem against NPRs, as their jump point defenses are mediocre at best, but having multiple player races displays the almost broken nature of jump points vs hyperdrives. Maybe a device that could create new jump points (for a ridiculous expense) would solve the problem?
The problem that I have (which isn't a big deal for most people, so don't take it the wrong way please) is that a technologically superior race (within reason) can send a fleet that is twice the size of a defending fleet that is technologically inferior (again within reason) and be defeated consistently. There is no counter to jump point defense except having several times the defending forces fleet size. Technological advantages help little (unless there is such a disparity that the superior force literally cannot be defeated, such as all end game tech fleet vs a conventional start fleet defending a jump point).
Unlike real life combat, with static jump points you cannot simply attack from a different direction, or "go around" or flank an enemy, you must plow through as there is no other tactic or strategy. This is especially apparent with dead end systems, as they can be defended almost indefinitely with a significantly smaller force of technologically inferior ships.
As others have mentioned, executing a squadron jump with appropriately teched-up jump drives is the way to beat a JP defense. I would say that while the current naval battle system is weighted entirely too much towards JP battles, they are a necessary mechanic in Aurora as they are really the major way a defender gains any tangible advantage over an attacker (the other possibility being to fight from orbit within STO range but this of course is a strategic defeat as the enemy will ransack your undefended colonies and lay siege).
There was an excellent suggestion made in the last big thread on this topic to tweak squadron jumps so that smaller ships gain a larger jump radius and larger ships emerge more tightly around a JP, which would preserve the importance of JPs as defensive choke points but allow for light raiding forces to be deployed which the defender must intercept with QRFs, adding a mobile component to warfare. I would favor this as it is quite simple and intuitive compared to many other ideas and adds a new dimension to warfare.
Another option would be to tweak the default JP network generation to have a higher concentration of loops. Currently it caries significantly but often the JP network is more like a tree than a network, which means there are often only 1-2 routes into enemy territory. A more interconnected galaxy with 3-6 routes to an enemy sector would mean the defender must spread out between several points while the attacker can concentrate, allowing a successful though costly JP assault to be somewhat less difficult to pull off. This would essentially be a simplification of the hyperdrive idea some have suggested in that it adds more routes of attack which can be exploited, but again without adding a complex new mechanic to the game.
Of course, the elephant in the room is that NPRs likely cannot deal with either of these things very well...game AIs in general struggle to handle multiple fronts and mobile/patrol warfare even in major releases from large studios (looking at you, Paradox...), so certainly if the AI in Aurora were to handle such things it would be a miracle on the part of Steve. The present system works for the AI which is an understated benefit, and my impression is that Steve intends the spoilers to do most of the work as far as changing things up from what would otherwise be an endless sequence of JP assaults.
I did consider using squadron jumps to give a little distance but that again works poorly against play controlled races, as I was playing both races and simply spread the defending ships around the jump point. It finally became feasible once I got the attacking race's squadron range up past 1m km but that still required 2:1 attacking ships (1-2 tech levels more advanced than the defending ships). To recreate, just split the fleet up (or use offsets) so that the smaller fleets are 60k-500k km apart or so (depending on tech levels of course).
For PvP campaigns I think it becomes necessary to establish house rules in any case, as the game is too exploitable by players otherwise. For example a house rule of JP defenses being only located at the JP rather than in a defensive net may be necessary. This may seem quite restrictive but can be necessary and actually can design space for more interesting strategies and ship designs purpose-built for this kind of JP defense. Others who regularly play PvP I'm sure can share many examples of house rules they impose to keep the game varied and interesting - no box launcher spam being a common one, I think.