However, some years ago I worked with 3D software like Lightwawe and C4D and despite the two programs have a GUI like yours, they also keep a tree like alternative very similar to Inkscape Filters editor. I think it's very important to give the user the choice of his tool in function of his mind ; this isn't only a matter of learning but it's also a question of personal ability. Aren't we in free software world ? 

Forgive me if this is just flamebait, but I think multiple options for the same function is usually a bad idea. Sure, OSS is all about choice, but more often than not (without having done extensive research on the subject), one very-well-designed option that everyone stood behind would have served the community better than 2 or 3 choices that cause endless disagreements.

With two tools that achieve the same functionality (under the hood), you just have to maintain more stuff. You have to have two sets of developers. New features have to have two sets of UI elements developed to interact with them. New code has to be tested in two places. Documentation for new users becomes hard to write without making it confusing.

I believe the underlying filter framework is great, and the UI is mostly workable. I believe to bring Inkscape's filters to be as good as the potential provided by the underlying filter framework, the changes don't need to be as all-encompassing as some of the things being discussed in this thread. I think the following list would remove almost all of the barriers to using the current filter system:
I know some of these things are what everyone's working towards anyway (eg reliabilty & performance), and of course it's not always possible to achieve perfection here! But I just though a list might be helpful.

 - Bryan