I think the main thing is that many other packages hide a lot of the complexity initially, and let you dig in as far as you need.
I think the outliner is finally getting to point of good usibility working with modelling layers and grouping, but I’d still rather layers be integrated, dynamic and nestable group/layers instead of 20 fixed layers and groups being a separate function. I had hopes they would introduce that with 2.5. Even though there seem to be advantages to the way things are now, I think it’s more accomodation to the limitations than real advantage. [edit: Looking at the outliner in 2.5 again, maybe it’s more integrated than I thought.]
Yes, same with materials, Accessoire. Working with simple materials and textures is still way too complicated compared with other packages. I’m not familiar enough with more complicated subjects like nodes, but almost all of the packages have nested functionality instead of Blenders network. You can’t share datablocks as easily in most other packages I know of, but then, I don’t think you usually need to, so it’s not much of an advantage. Nested layers of settings is a lot simpler because you can hide a lot of the deep functionality with presets.
I also still wish Blender had the tool icons (especially context-sensitive ones) that most other packages have, but that’s never gonna happen Not sure if I like the new Tools shelf yet, haven’t used 2.5 enough.