Things I've found...

Here are some thoughts about work flow in the current SVN of Blender 2.5.

Skeleton Sketching | Constraining the sketch to a volume's centre requires CTRL held which is not explained at all clearly.

Weight Painting | Need to be able to convert mapping data to vertex data. Noise maps baked into verts of weights painted in grey scale in Photoshop (or gimp :)) to be applied and converted to weights.

Particle System | A particle system can be re-named but the name is not reflected in the modifier stack.

Preferences | Default preferences more consistent with 3rd party apps. Turntable VS Trackball for example. Another example is having to select UV over generated every time you add a bitmap to a material. If a UV exists, it should be the preferred mapping system.

Paint modes | On selection of a texture, the brush button under the texture tab should be on automatically. Brush selection on the left tool panel should sync with the texture panel on the right.

Rendering | Cannot set up a BG image in a render without post compositing it. Makes it difficult to set up a Bg to reflect into materials.

Viewport | Cannot hide the grid in non perspective views.

Materials | There is an 'add material' + button but not an 'add texture' + button.

Materials | Multiple materials (and textures) create a scroll bar but there is no way to resize the window to show all.

Materials | Animated textures don't automatically set themselves to the full frame range of the incoming clip.

Nodes | A check box to turn off colour management in the node view is needed when working in a colour managed scene. Otherwise the materials are hard to see.

Graph editor | Need to be able to drag on and off channels (the same functionality as the 'show/hide layers with a mouse drag' in Photoshop.) There is too much data to spend the time clicking on and off each lock or eyeball individually.

Sequencer | Proxy file paths are currently stored with each clip which can be painful if you have many clips to import and work with. A global proxy path would be far superior.