Project management software for R&D projects

[SCRawl]

I have a friend who works as a research scientist for a multinational manufacturing company. He has become frustrated with using MS Project to manage his projects, and so asked me for advice about whether or not I know of a product that would suit him better. This is what he says he's looking for:

I know people who've been in professional project management for decades, and they mostly agree that MS Project more of a pain than a help.

I would not necessarily go that far, but the fundamental problem is that classical project management approaches are not suitable to R&D projects, which are full of decision points, also Project doesn't have logic, only time relationships. MS Project is convenient for Gantt charts (which my upper management doesn't really believe in, not unreasonably in my opinion) and resource management (which I don't really use). I am looking for something that combines the functionalities of flow charting with Gantt, with visible notation (like mindmap) and good file linking. It would be nice if the file and its links were searchable, but the latter is not critical.

I'm a programming student now, but I won't be near the level of ability to create such an application -- even for just personal use -- for a while yet, if I ever get there. Does anyone here know of a product that would suit his needs?