That's for "pure" puzzles though. I'm not actually sure what you're thinking of there (if challenge rooms are testable yet in the dev build, I've not had a chance to try them yet). I'm thinking of the sort that's like, I dunno, block/switch puzzles or mazes or stuff like that, and that's all there is to it. You know, the "pure thinking" sort. If you mean "puzzle" as in "HERES A MILLION DEATHRAYS, DONT GET HIT, oh and hit those two switches, thanks" that's a different story. Half the time I don't know what people are talking about when they refer to puzzles nowadays. Like how every platforming section in any game is a "jumping puzzle". That damn term confuses the hell out of me.
I mean in the sense that the player has to, at some point, say "Oooh, I gotta do X" but that's not enough, they still need to actually do
X which is still going to require their wits and reflexes in a bullet hell sort of way. (e.g. "follow this path" like we have is too simple)
For example, take the rooms full of one-way floor tiles, right? Now in the center with the chest, put a blaze cannon.
The puzzle is figuring out the path necessary to reach your destination. But you've got to walk that tight rope while also dodging enemy fire, which might make you fall off and have to start over.
I mean, yeah, we've got those rooms with the rotating turrets but those rooms aren't nearly deadly enough. Sure, a few of them I ignore, but that's because they've gotten to the point where there's so many bullets, a safe path doesn't really exist at all (and the designer said as much by putting 3 health pickups on the floor).
In terms of secret rooms, there should always be some level of ambiguity to opening them. In Issac its the chance that there's too many possible locations
and the player doesn't have the resources to check them all. I'm looking at it from the point of view of the trigger conditions being unknown. As in, some aspect that the player can't be aware of, but that despite that, can still trigger the room by performing some action. You'll jump up and down and spin around and muter "Alakazam" a few times, and if it doesn't work this time, you'll try next time. And about half the time it works. You don't know if it's the jumping, the spinning, or the magic word, where you're standing, or the phase of the moon, but gosh darn it, it works
The problem right now is that I'm almost always disappointed to get a secret room instead of a health shard. Sure the rewards are generally worth looking at and taking one, but 90% of the time I'd rather have the health shard.
Also remember that we have a thingie (a "restriction"? whatever those start-of-level things are) that shows you where the sac room is
. I think there's a perk for it too.