I disagree with your reasons why this is a problem and how you have presented it, but the new economy has certainly done little to meet the promises it was meant to fulfill. This economy ruins the game because the AI has no clue how to run it, and the old method of throwing production bonuses at the difficulty levels actually just helps them build a deeper hole to fall in once the initial territory grab is over.
I also agree that the early game exploration is one of the best things Stellaris has going for it and 2.2.x has nerfed a lot of anomaly awards while the new economy makes space based resources very noncompetitive until you research 5x +10% techs, and even then a single additional planet will provide almost as much as your 50 systems do. The market is also a huge crutch that nullifies any difficulty the new system brought.
I'm with you on the feeling that conquest gives very little incentive where either I amalgamate an additional 500 pops and work through trying to get them all where they are best suited from an egalitarian perspective or dealing with 10planets being purged for 10 years and having to manually remove all buildings and districts to reduce the upkeep and sprawl. Unless there is a leviathan or really nice planet in their borders, I find I am very disinclined to mess with my neighbours. I remember a long time ago with one of the many reiterations of strategic resources that Paradox said they wanted to make them worth going to war over, and yet here we are with version 22 of these resources being broken and rebuilt from the ground up, that only 3 of them actually matter and the really rare ones give a single edict with a single use(if you even go for megastructures or late game tech). The trader enclaves, a paid feature, are now just a fixed cost version of the market that you have to go out of your way to find the right one depending on your needs.
By making planets the be-all end-all of both basic, advanced, and strategic resource production there is no real reason to be anything but isolationist and turtle on a few worlds. No reason to step outside your borders until the very end game when you are looking for FEs to steal from or leviathans to kill. You just get one mineral world, one farm world, an ecumenopolis/forge world, a research world, and wait for megastructures. Anything more will just be overkill. All the other empires are speedbumps on the way to a late game that barely runs and has 2/3 of the crises not functioning at all in the current release, and with how they use the current economy in vanilla they aren't even that if you don't gimp yourself with an RP built empire.
Maybe a balance patch will solve some of these issues but 2.2.x has added so many problems and broken a lot of things that worked in the old system there are bound to be a lot of things that slip through the next few patches unaddressed. I like what the new system could be, but that's how I felt at 1.0 launch and here we are with a new load of potentially good features that only time will tell if they fulfill it before being axed in favour of more potentially nice things.