I suggest that all diplomacy-related events that currently run once per construction increment (trespassing, diplomatic ships, establishing communications) should be triggered every increment, perhaps with the same cutoff as standing orders (3h+), with a diplomatic score adjustment based on time spent maintaining contact, or on increment length, whatever is more feasible.
As far as I understand, this shouldn't be too performance-taxing (only checking for current contact is necessary for all three), but that would be definitely worth it given how it's currently possible to intrude into alien territory without consequences, or fail to inform an NPR of your claims on the system, as long as the offending ship is outside detection range when the construction phase ends. This also means it's technically possible to enter an NPR home system and land troops on their homeworld before war is even declared. I was going to suggest that NPRs issue a harsher diplomatic response upon their colonies getting approached, however I see you've already considered the possibilities
here and decided against it. I understand the concerns associated with player ships accidentally passing near a xeno colony, however approaching an alien homeworld is something that really doesn't happen by accident short of neglected geosurvey ships, so it wouldn't be far fetched to say that a NPR detecting 10kt+ of alien ships within 10mkm of their homeworld should result in an instant declaration of war.
Additionally, I would suggest that interrogating POWs of a race whose language has yet to be translated would trigger alien communication events instead of contributing to the intel score with a 80% malus. This could be restricted to the races with whom communication attempts are already underway (which are currently on by default, and can't be cancelled, maybe clicking the "Communicate" button in the Intel window again should cease the attempts?). I'm not sure whether it makes more sense for it to happen upon lifepod pickup or during proper interrogation in a naval headquarters - in any case, defeating an entire NPR's navy and capturing thousands of prisoners without ever having learned their language was certainly a peculiar experience!
I would also suggest that conducting an autopsy on an alien species would add said species to the empire's Race Information window with a population of 0, complete with full species data and an ability to create colonies for said species. This way one wouldn't have to resort to DB editing after boarding an alien colony fleet with a million colonists yet nowhere to unload them. In a similar vein, actually adding class designs for boarded alien ships into the Class Summary section of the Intel window would be very welcome, as currently one needs to switch between two windows to assess the capabilities of an enemy fleet where some classes have been boarded before.
In the Intel window, when a ship class is selected, and some ships are marked as destroyed, is it possible to continue to show the systems where those ships were (apart the wreck marks in the galactic map)? I can think to go and salvage them later, and their location is useful to remember of them.
Moreover, if I salvaged some of them, could these ones be marked somehow (let's say, using an asterisk or adding an "(s)" near the ship in the Intel window)? This mark should be valid only for the ships salvaged by me, as I don't know if a NPR did it, so adding a factor of uncertainty in perfoming these operations in systems controlled by an ostile NPR (I need to survey the system in anticipation, before mounting a mission).
I admit it's not the same, but you can double-click any ship in that list to focus the game on its last known location, even if it's long been destroyed or even salvaged.
addition would be variable firing range distances. Once the firing distance of a gun has been explored, you position yourself outside that range and nag away at the enemies defences.