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Blender 2.5 has changed the UI significantly from the original commercial version, and most comments I read about it say that it has improved significantly. Blender the open source project has changed and grown so much bigger than Blender the commercial product that they are totally different.

Regarding hotkeys, there were some major changes for 2.5 along with other UI changes, but after that the default have barely changed, just additions and minor changes when the underlying features change.

Making hotkeys remappable was in no way a solution to that "problem", it's a standard feature in other 3D software that a lot of users requested, especially those who wanted to make the hotkeys compatible with Maya and 3ds Max.