Your question might be a little to specific for general discussion section, but i'll give some insight.
A pretty common method of traversing mountains in RPGs would be making a mountain pass.
For the player, ascending and descending can be a lot of fun, because you are getting that feeling of perilous hiking, among anything else designed.
For the developer, a mountain pass can have countless interesting little things to make it special.
Hazards, bridges, jumps... terrible creatures may live on the mountain. Or maybe a friendly tribe?
Generic design ideas:
- A threat/X is terrorizing/X a mountain region, and if killed/X, a tribe/X will let you pass through the area.
- A bridge/X is broken and you must find a way to fix/X it to pass through the area.
- The region is naturally almost a maze with cliffs and steps everywhere... while the player tries to find the right path, perhaps they could stumble into treasure so dead ends aren't a waste of time.
Parallax backgrounds can give the illusion of being high on a mountain, with either a sky or distant land below. Forcing the player to traverse terrain up or down cliffs is a great break in monotony from maps which are mostly flat.
Important Note: Readability and landmarks are crucial for complicated regions. Giving them something unique to look at will help them remember what is there, or if they haven't been there yet.
Hope that helps.