Unity "free" is superior to GameMaker in virtually every regard, and the Unity Pro version, which costs three times as much, is a significantly more capable platform.
I remember using GameMaker years ago, and was very pleased when I made my first "game", and all I did was use couple of basic features. For the things I am interested now (simple 2D games), GameMaker seems like the best choice. When Unity 4.3 goes out, I'll check it out and see how it compares to GameMaker based on my requirements.
I'm sorry, what?
Windows uses Direct3D for the native UI, and OS X uses OpenGL for the same thing.
If you're doing AAA games in 2D, yeah you will use the GPU. But an indie game? You probably don't need it. Especially if you're writing the game without Unity (i.e. straight C++). The costs of setting up and working with 2D in OpenGL is high. I've done it. It's not fun, it's not pretty. It's a bitch, plain and simple. Texture atlases, font rendering, UV coords, texture uploading, vertex buffers, shaders. That's a ton of crap you have to worry with. Just to render simple 2D sprites to a screen. Many people can and do skip it and go straight to SDL or somesuch. It works, and modern CPUs are more than adequate.
This isn't just about performance. On a phone it's about not burning the battery down by loading down the CPU with expensive tasks that the GPU can do more easily.
Don't forget you can do your font rendering in the classic environment, then ship that texture image over for placement. It's not all that difficult with the right tools, many of which get packaged up for you transparently. You're not stuck in OpenGL by any means.
Most "2D" games are just 3D games rendered in isometric mode, top-down, with the depth information being used for layering.
Yes, but let's not forget you made it about performance.
There are plenty of reasons to choose to use OpenGL. Lots of freebies come with it. But you can still do 2D games without the GPU. That's the point. You can't just keep moving the goal posts however you want.