When using the online UI, changes I make are dropped and not merged when a new version generated by the desktop tool is uploaded. I'm presented with a 'Save as/Discard/Overwrite' option menu, when what I really want to have an automatic merge of the two documents happen in the background.
Sounds like a reasonable enhancement, if the differences aren't huge and independent, then probably the documents could be merged without problem. If they are clashing, that makes things more difficult, but I guess only supporting independent changes would do for starters.