The thing that frustrates me most in IntelliJ is that all of the dialog windows are modal for no apparent reason. Why can't I focus the main window or at least interact with it to change tabs, select text, etc when I have dialogs open?
"Find in Path" is a particularly obnoxious example: it's fairly common that I want to search for a string fragment, so I open the search dialog and set up my search context, then try to select text to copy as the search term, but I can't, so I have to start over.
I want to be able to interact with the editor at all times, though I could see locking it during complicated refactors to keep me from changing code while the IDE is trying to change it too (only while a progress bar dialog is visible).
Modal windows should be the exception, not the rule.
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To be clear I love IntelliJ. While I prefer simpler editors in many situations, I can't see myself going back to anything else for medium-to-large JVM projects (Scala especially). The modal niggle and a few other minor usability issues are small blemishes on an otherwise great IDE.