Just finished this morning and started on my Recursion play-through.
Although I enjoyed Bastion for what it was, it's mechanics didn't draw me in the way Transistor did. Mechanically, my favourite part of the game was coming up to an Access Point after unlocking one or two new Functions, and unequipping everything to starting on a new build. Looking for synergies between the various Functions, and then being able to pull them off in combat was deeply rewarding (Crash(Bounce())+Flood(Get())!) and you can see that SG put a lot of effort into encouraging and rewarding players for trying out Functions in different ways. The only criticisms I have of the gameplay are that playing on a controller made Turn() planning frustrating, since most Functions auto-lock on nearby enemies. And secondly, when in the various sandbox tests (particularly speed), you can't view what you have equipped which tends to needlessly obscure the solution.
From a narrative standpoint, I think SG wants us to work at it. They want us to play through multiple times to hypothesise about the world and try and verify our interpretations through the additional content. And yes, Recursion mode is quite different so far. Also, I appreciated that the traditional antagonist structure was ditched at the second act to great effect. I'm still digesting the story and will continue to think about it while finishing up my second play through. Ultimately I might decide that it doesn't achieve what it's trying to, but I'm not able to make that decision yet.
Overall this is such a great package; easily the best thing I've played this year.