Thanks for the detailed and thoughtful feedback, it's always welcome and very useful to me!
Your feeling of the game is certainly valid, and I think a big part of it comes from the setting I chose, even more than the scope or timeframe. A sense of place is very important to me and I've built this world to make sense, which imposes hard constraints. A deserted submarine station just couldn't get as weird as my previous games. I still tried to have as many cool details as possible, as you're right it's something I value highly, but it was almost exclusively left to the codex entries and a few secret areas. Even when expending the jam version later I felt a bit restricted by that setting, both in term of space and narrative.
I'm a bit sad you felt the aliens come "out of nowhere", considering all the foreshadowing I tried to add, but again it's almost exclusively in the codex and I can totally imagine players not thinking too hard about it at this point of the game. That's something I tried to reinforce with the few dialogs I added in 1.0.3. A way to encourage players to stop and read back the entries they've collected to try to piece the twist together before it actually happens on screen.
Other than that, I did nerf the health drops from the lights and other props in recent versions. It was a way to make the Whisky Flasks more useful. But in the end I'm fine with players being able to farm health if they want. I don't really enjoy the trend of Metroidvanias embracing Dark Souls' difficulty (I love those games but they have a different focus) so I'm aiming for something closer to Metroid or Zelda, where health is relatively easy to come by.
I'm not sure how I could address your feeling that many of the abilities are just differently colored guns as it only accounts for two upgrades, both optional. The game still have dashing, sliding, double jumping, diving, a grappling hook, homing missiles, waterfall climbing and heat resistance. They should feel relatively memorable and it's a problem if they don't. I feel like they're all used extensively, so if you have more feedback on that front, I would like to hear it :)
About the jam itself, I talk about it in my postmortem but the short of it is that I'm not really interested in game jams as pure design exercises. I wanted to see if I could make a fully-fledged Dreamnoid game in a month and change. It was more of a one-off 'production' exercise and I've no plan to join more jams in the future.
My next game will probably be a sequel to both The Lightkeeper and The Trespasser and I will definitely keep your feedback in mind while I make it ;)