I'd like to eventually learn to make a simple 3d engine suitable for a retro FPS. However, to start with I'd like to learn how to make 2d engines for side scrolling or isometric action games.

Basically, game dev is a hobby for me so I'm in no rush to actually publish a game. I'm interested in learning nearly every aspect of how games are made.

I've already been playing around with Unity and Game Maker Studio a bit. I'm continuing to learn Unity but rather than spending tons of time learning how to use a game engine's libraries I would prefer to learn how these things are built and make one myself.

You might find it valuable to make some simple games without using an existing engine. For example, a simple action platformer game is nice because the physics can be pretty simple.