Puzzles that make more sense: ideas

[Astefia]

I wanted to return to the old fangame project of mine, and thinking about it gave me an idea.
So, all those Team-something lairs that are blocked by puzzles. They don't make much sense - any intruder who's into puzzles can easily break them? and a member will waste some time solving them. Especially those spinny tiles at the Rocket hideout - why are they inconveniencing themselves?
But what if the puzzle will turn into a password hint when combined with something more private from the intruders?
For example, in my game the protagonist in the evil team member running away from a raided base. I'm thinking of putting some notes in the different rooms of the base, that, put together, will generate a password for the secret escape door using the Pokemon the protagonist has at the start of the game. (For example, "Number of letters in my flier's nickname multiplied by how many of my mon are in Dusk Balls")
Is this idea any good? Are there any more ideas of puzzles that just make sense to exist instead of just mazes or block-pushing or "find this key item to unlock this door"? (Not counting gym challenges, of course).

 

[AenaonDogsky]

This is always hard to nail down right. In the end games are games, and baking non-gamey puzzles intrinsically into the game is gonna be difficult work. One way to approach it is to think "how would I prevent someone from raiding my base". If someone is using an actual physical obstacle, perhaps a mon with enough weight can go through it. Hacking and lockpicking minigames assisted by a pokemon's ability could also be used. I guess moving boxes around in some manner (to make way) too. Perhaps arranging certain objects in a certain way to open a door (with hints like you've mentioned).