I think you're underestimating the complexity of what can be in a makefile. If you allow a user to hand-edit the generated makefile (or to have created the original input), then all bets are off. Depending on which version of make you're supporting, the language is turing complete. and lets you do pretty much anything. Creating a GUI that can parse/understand/edit/maintain that is not a trivial task. It's not even a difficult task - it's insane.
It would be insane to actually maintain the whole file. General parts of it though, like rules or commands could be taken as 'Name:Value' or input fields in the GUI. Adding files or dependencies would be mostly GUI, allowing you to select files or directories.