I don't personally think the IDE limits you. I've used Visual Studio in the past for my fairly extensive C++ development, and for programs that are, like, over 3 Mb in size, yes you need good organization.
But for 32 Kb of code? Not so certain that the IDE limits you there. The IDE is basically a text editor. It doesn't really add or remove from the underlying compiler which is the avr-gcc compiler.
I don't think the font, the font size, or the colour of the text is really the issue standing between you and a nice working project.