I wasn't expecting to see INFRA mentioned but it's one of my favorite games for a lot of the reasons you mentioned! It really had a sense for exploration and environments to tell more of the story. And it really is part puzzle game without having any single gimmick like other first person games. It reminds me a lot of Half Life 2's puzzles (which makes sense since INFRA was also built in Source as far as I can remember).

I'm really itching for more expansions or games like it. Not sure what happened to the DLC they were working on, but there were some groups working on mods.

I recently beat Antimatter Dimensions after coming back to the Reality update after a long while. There's a lot of depth, especially in the new additions. I appreciate all the layers and addition of QoL upgrades.

Bitburner was fun as an incremental hacking sim. I haven't played it for a while, but I find it really unique.

There's also Orb of Creation which can be a bit grindy but also seems really fun for what it offers. I've been playing the demo version at https://marple.itch.io/orb-of-creation

I haven't seen any incremental games get posted. They aren't exactly traditional games, but so many of them are open source like Antimatter Dimensions or Synergism. Bitburner is a unique one as an incremental hacking sim, since it relies on actual scripting to grow and automate tasks.