Developing a medium-sized game takes an unholy amount of time. Logically, this makes your toolset a crucial factor because the tools' productivity and your mastery over them will dramatically affect the process. Most areas are already covered by brilliant tools: tiles for level editing, spine for skeletal animation, Physics Editor to create rigid bodies, the Libgdx particle editor, and the list goes on.
However, you might have certain requirements that no existing software features yet. Beware, the never reinvent the wheel advice is really good advice. Think about it; if the tool closest to what you need is open source, it is probably more convenient to check out the repository and add such a feature yourself. The community will probably be quite grateful for this and you will get public recognition!
Alright, if you really need something completely different, the best option can end up being implementing a new tool from scratch. This...