I'm currently building a 3D platformer (like Super Mario 64, Banjo-Kazooie) using Blender and Unity and I'm finding it somewhat difficult to design and build a 3D world suitable for 3D platforming. Right now, I have a list of areas that I would like to see in a level e.g. giant fountain, sunken ship, courtyard, etc. From there, I draw a map on paper and write down where I want each area to be. That's not too hard to accomplish, but the difficult part is turning that into a 3D world that feels good for platforming. I've been using Blender for a while now so the issue isn't whether or not I can build 3D models. What's a good process for designing/building an entire level from start to finish? What are some tips and/or pointers you find helpful that may help me in designing/building a 3D world?

Any help/advice is greatly appreciated.

Have you created your avatar, the character the player controls?

If so find how far they can jump, reach, interact and use this information to start the construction process.

If you answered no to the first question, while that is where you need to start.

The most important part of most platformers is the path the character takes through the world. Put together a testbed (can be as simple as a set of stacked blocks), and figure out how high a ledge your character can reach by jumping, how far can they jump across a level gap. Further, figure out what distances constitute an easy vs hard jump (does a certain length/height of jump need a running start, does the player need to crouch at the apex of the jump to make it?).

With those in mind, you'll want to sketch out the sequence of jumps, and how they tie into the geometry of the level. The fountain level might contain a spiral of jumps leading to the top of the fountain, the ship may require the player to leap along the rigging, etc.

but the difficult part is turning that into a 3D world that feels good for platforming.

what doesn't "feel good" about the test levels you've created so far?

as navyman says, you really need to be able to test the levels as you build them.

are things not a proper size and / or distance apart for a platformer?

since jumping is a primary mechanic, setup of jumps is very important - as mentioned by others. proper distances would be determined based on the players movement rate when jumping or experimentally, then repeatedly tested and adjusted until they "feel just right".