As we're using .46, here are some issues that have arisen (some pre-date .46). Should they be added as RFE's?
Sodipodi absolute paths - if you add an image, then delete it, the old image absolute path seem to remain in the file. Maybe it's the sodipodi namespace stuff. In fact is there a good reason for both an xlink and sodipodi:absref for the same image - seems like unnecessary duplication and chance for bugs.
Effects|Modify Path|Color Markers - In .46 it's giving a weird warning message box (maybe it is being fixed) and does strange things like accessing the sodipodi full paths (see above). This effect has always seemed to be a kludge since stroke color should be applied when end markers are chosen in the object|fill & stroke|stroke style dialog
Effects|Render|Grid - This is confusing. the right grid and guides are in document properties. I used the effects grid by mistake, then couldn't adjust it - had to undo. If the Render grid is for fill shouldn't it be under the object|fill & stroke |fill pattern
Open Icon - the blue folder color is very similar to the old save icons (with blue floppy disk) thus, I keep clicking the wrong icon for save - the open folder color should be tan (manila).
Object|Fill & Stroke|Fill gradient pattern - trying to use the awesome gradient tools more and I find there is an inside out gradient but not an outside in gradient and I can't figure out how to switch it. This also applies to left-right vs right-left (including the gradient adjustment tool) - this can be worked around by flipping the object but that's kind of kludgy.
Finally here's a perfect patch opportunity for a newcomer wanting to get involved: Object|Transform|Scale - switch default scale proportionally to checked - this is a simple gtk checkbox setting