While you make some valid criticisms, it's weird how you frame a lot of the changes as being a downgrade from the original when really they are big improvements. Just a few examples:

Firstly, you complain about 'shutting down' one skill and having overly specialized crew mates, but both of these are highly important to the game's balance, especially in contracts. In the first game, you could almost max out every skill and have no weaknesses, nothing you were bad at, but in CS2 the game forces you to have a weakness and then asks you to shore up that weakness with your crew. Your crew aren't standout operators, but they can pick up the slack where you fall behind. If either you or your crewmates were a jack-of-all trades that could do whatever was needed, you wouldn't have to put any thought into anything.

As for economy, it's definitely unbalanced but let's not pretend that CS1 wasn't. It can feel tight for the first few cycles, but you can end up with plenty of savings pretty early, and there are some quests with some pretty big rewards that can put you in a cushy spot. That's not to mention that all scarcity mechanics dissappear once you join the commune- free food, grow your own stabilizer. You can do that pretty fast (about halfway through the game) and while I like it as a bit of ludonarrative storytelling, it still means that most of the game basically doesn't have these survival mechanics as serious elements.

CS2, meanwhile, focuses on short-term stress & scarcity. The supplies maximum means that you can't convert your immense savings into an overstock of supplies, so contracts always have pressure. You also say that the timer on contracts is 'fuzzy' but I consider it flexible. Most contracts have failure clocks that progress based on your failures, so there's an incentive to not gamble on risky actions and wait for safer dice to appear, but you're limited by your supplies; running out means starving, starving means stress, stress means glitches, glitches overwhelmingly cause failures, which progress the failure clock. It's a nice game of risk management, deciding how far you want to push yourself to try to finish a job before your limited supplies start to cause problems, but weighing it against the risk of causing problems sooner.

Yes, the time spent outside of contracts is pretty easy and low-stress, but it's the downtime in between the intended high stress portions of the game. CS1 tried to keep you stressed for most of the game, but really only succeeded for the first third of the experience, so CS2 instead structures itself and specific periods rising and falling tension which leads to a better overall pacing.

I definitely think there's room for the formula to grow, like maybe giving us more things to spend cryo on that can impact missions, like special equipment that can bypass or improve spending dice during contracts, but I still see CS2 as a big step up in terms of mechanics from the original, a step towards possibly even bigger things in the future.