I actually put my Godot project on the backburner several months ago as I was having major issues with v-synch issues on Android and Windows. I was also finding the collision detection system not up to scratch for 3d kinematic objects. The Godot scene system, whilst very powerful, can do your head in with its complexity at times. In theory it is more powerful than the prefab system of Unity(since you can nest one scene inside another), but the fact that you can can only view/edit one scene at a time is frustrating!
Instead I decided to invest time in a more obscure and simpler open source 3d editor called Zgame editor. Not much documentation, but very easy to use if you want to create a 3d Android game. The exporting/testing to Android is very streamlined and works well, but there is no ad or in app support. Still worth checking out for your first foray into 3d (especially if you want to do an Android game). There is currently no scene editor, so it is for more basic 3d games. The event system and scripting language is very similar to Gamemaker, so you will pick it up in no time if you have used GM:
http://www.zgameeditor.org/index.php
Another open source IDE to look out for is Polycode, which has been taking its sweet time to get finished but hopefully there will be official binaries soon! It also does 3d and 2d like Godot, but uses Lua or C++. It has a very nice IDE/GUI as well:
http://polycode.org
I do intend on getting back into Godot when it is a bit more mature, but for the moment I will spend more time learning Unity. The core principles translate over to Godot surprisingly well, since Godot has taken a lot of inspiration from Unity. The advantage of Godot being that it is free/open source and has a true 2d environment as well as 3d. You can also mix and match the 2d/3d in crazy ways. If you look at the sample projects, there is a 2d pong scene done in a 2d scene that is then used as a texture mapped to a 3d object in a separate 3d scene...all in realtime. You can also go the other way around and have a 3d scene remapped into your 2d scene..very impressive!