Ever since I have switched to Intellij from Eclipse, I have had this feeling of 'not normal' inside Intellij's UI. Something about Eclipse's UI always felt more 'natural' and 'precise' to me.

For starters, the Intellij IDEA IDE is written in Swing which uses custom UI widgets. Eclipse is written in SWT which is able to use the underlying Operating System's native widgets.

But what exactly is that difference that causes Intellij to not feel native.

Its not performance

At first I thought that Eclipse, due to using native widgets, would be performing better and thus feels more natural. Turns out, that is not the case. Intellij's UI is in fact snappier than Eclipse.

Then after some exploration, I eventually stumbled upon it.

Highlighting of elements under cursor

Move your cursor over the Project view tree in each IDE.
Here is a gif showing the effects:

Intellij:

Eclipse:

Notice as I move the cursor, in Eclipse the items underneath get highlighted, in Intellij not so.

Turns out almost every view in Intellij, is a tree view. Example - File Structure, Version Control, Gradle, Project, Debugger, etc, they all use a TreeView component to render their contents.

The fact that the tree items don't get highlighted in Intellij when you move your cursor across them makes the UI feel less 'precise' and more 'un-natural'.

Bug
I have opened this bug with Jetbrains to address this.
IDEA-151128

I notice that OS X doesnt highlight tree items on hover either, so this is felt mostly on Windows.