regarding player invading markets, it should at least not happen instantly, the progress bar could return imho, personally i just outlaw player invasions (the same way i outlaw waiting for a faction to start winning the game only to use agents to then make them my friend) i find requesting an invasion fleet and escorting the landing armada in more interesting in any case.
something i want to bring attention to however is that in my current game of about 5 years NONE of the factions have been wiped out, i wondered for a while what was causing it, and it seems that systems with PIRATE bases just cannot be invaded, this is because the invasion fleet gets stuck on chasing pirate fleets and fighting the pirate base, leaving not nearly enough strength left for the actual invasion, and this is only relevant if the chasing of pirate fleets does not cause the invasion target to sign a cease-fire agreement before they even get to the target, something that happens over 90% of the time (i have followed invasion fleets around many times by now)
to fix this in my own game i ended up turning allow pirate invasions to true, this way the pirate markets will eventually be conquered by a non pirate and allow in or out of that system in the future, i do not play a pirate play style, preferring to pick a faction and try to make it win the game, but i can imagine this solution not being very nice if you want to be hostile to the civilized factions, as you would only have the spawned pirate bases far away as markets to sell or buy from
a fix to this could be to make invasion fleets consider pirate bases in their star system and the destination star system and get a little bit extra strength to compansate for this.
another solution would be to make invasions BIGGER in general, but cause an accompanying "counter invasion" fleet spawn at the invasion target, this would allow to make invasions large enough to swat aside pirate presence, but still have a balanced space fight with the defenders (besides i actually liked the giant fights on the first few patches of 0.9 nexerelin, this would allow for random invasion sizes again, as you could just spawn an appropriate counter-invasion fleet if the invasion is randomly very large)
i think mby invasion fleet buildup could be slow, but states of war end very fast, so mby this is something to look at as well, factions that are at war without a positive diplo event should stay at war a bit longer imho, but if there is friendly relations events then they should stop fighting fast imho.
another thing that bugs me a little bit is that the diplomacy events happen all the time making it hard to keep track of with many factions, i would like if diplomacy events happened at a constant global rate, rather than once every so often per faction (so more events with more factions) the factions involved in a diplo event can still be rolled randomly so it does not feel mechanical