My background: game dev since late 1990s, used Unity professionally since 2014, previously made my own game engines/frameworks (C/C++/Java).
NOTE: I started compiling this list when the most recent version of the engine was 4.2. I've marked instances where the things are clearly addressed by newer engine versions.
Without further ado, in no particular order:
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AnimationFrames:
When creating new animations, selecting them and pressingF2
to rename:- Doesn't rename the animation but the selected node from scene tree, minor usability issue there
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Script editor and/or GDScript