Well there's puzzle modding and there's making your own puzzles. There's also modding puzzles for maximum fun or modding them for maximum functionality (make speedcubes better). I've done all of which, and it's loads of fun. With those in mind, you can narrow down a project and get started.
If you just want a 3dprinting/cubing project it's great to print a 3x3. Square 1's are also a lot of fun because it's pretty easy to design a functioning square 1 and it doesn't take long to print. There's also the great world of shape mods where you can print a fun shell for an old 3x3 you dont use and then you can have a 3x3 puzzle of any object you can think of (fruit, character heads, etc). One of my most popular mods is the corn cube I made, a 2x2 that looks like a cob of corn lol.
In terms of using 3d printing to make speedcubes better, you'll definitely be looking into 3d printing mostly core magnet kits for cubes you wish had core magnets. For instance, I wish my qiyi MS had core magnets so I designed and printed the necessary pieces.
If you want something really basic, definitely look into shape mods for something fun. performance wise, looking into core kits. Lemme know what type of things you're specifically interested in, I'd be happy to help. Puzzle modding, in my opinion, is the coolest part of cubing.