I am a Arduino User. I had experience in working with many other IDE's like Keil, CCS, IAR.
There are few changes I like to suggest:
GUI interface for Optimization Flag: Add a small GUI interface in preference section for optimization flag settings.
Option to add multiple .c & .h in workspace tree. Files added should appear on project workspace tree on left side. Write know you can also add multiple files but there is no proper project workspace tree like section.
Display ZI, RW, RO & Code data separately. This could be good if there.
When right click on any variable/function, it should have option to take you to its definition.
Make a copy of all internal library used and move them in project workspace, & then build the code from these files which are in project workspace. Like IAR has option to "ignore standard include directories"
Most of people will say no it, but below I write some of arguments in its favour:
a) All the required .c/.h are in your current project space, which gives a better view what files are included are what are not
b) Sometimes you want to tweak a 3rd party library for some code related issues, at that times this option is good as it wont reflect in any other code. All library changes are in this project workspace only.
c) At any time you can check what inside any function in library to see what going on. If this is not the case, u have to go in default location and check which is not in workspace.
First 4 options, I think any IDE should have.
I dont know why arduino as IDE dont have those?