I stumbled across this old thread and couldn't help thinking it needed an update.
BC3 has been out for a while along with a new GUI and significant improvements:

bookmark
AM many
BC one
BC3 ten

merge method
AM via float button, cannot through mouse's right button
BC via tool button , and right mouse button
BC3 toolbar, gutter buttons, right-click context menu

edit
AM support directly edit
BC not support directly edit, can be edit through press F2(in bottom of editor)
BC3 full-screen editing

Quote Originally Posted by ;5390
Three way
AM support
BC no
BC3 True 3-way merge support:
Compare of two files against a common ancestor, auto-merging changes from both files into a new destination, manual resolution of conflicts (lines that differ from the common ancestor in both files).

Some compare tools claim 3-way merge support while actually implementing a 3-way compare:
Compare of two files against a common ancestor, manual merge of changes from one file into the other instead of automated merges into a new destination.

BC3 is still missing a basic 3-way compare