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Passive upgrades seems like an interesting design space you could explore. The potential synergies could help create more emergent gameplay and keep people engaged. Also, occasionally letting people get overpowered combos can help people who feel like they are bad or stuck make progress in the game.

Yes! This is something that we have in the game but is not in the alpha build right now. We call them auras. I've made a thread so people can discuss and post ideas for these!

I don't know how hard you want to go on the meta-progression elements a lot of rogue-lites have, but unlocking seeds based on various criteria seems like an obvious step in that direction. Kill X green flies, die in the last hole before a camp, that sort of thing. This can also increase engagement so long as it's paced well, and maybe keep people from being overwhelmed by seeds right from the outset.

In this aspect I think we're going pursuing a more Spelunky route than Binding of Isaac. One of our design goals is that a friend can come over to your house and play the game in the same way they play at home. However, I think your ideas are right on in that spreading out suits a bit more, and giving the player more sub-goals are things we want to explore. I'm hoping to explore some kind of mission-style structure you mentioned as a series of steps/prerequisites for unlocking teleporters to later biomes.

Speaking of green flies, I died to one in a camp... :(

Sorry, that shouldn't happen :( Their wall detection is a little wonky.

I think there is the potential for some interesting alternate game modes

Love these ideas. Seeded daily runs are definitely the thing that is most certain to be in the game. I also love the random starting loadout idea a-la Eden in Binding of Isaac.

Totally agree with the other items you posted as well!