Bumping mendeleydesktop to 1.13.1 works fine in an ~amd64 box. I didn't need to change the ebuild.
I already bumoped to 1.13.1 in the science overlay. Also version 1.12.4 is based on the ebuild I pushed to the science overlay. This was later pushed to tree by jlec. Somebody with the required privileges could do so too for version 1.13.1. If somebody is willing to import the ebuild from the science overlay, please keep in mind that I adjusted the license. This currently discussed in bug 536686.
Please see http://support.mendeley.com/customer/portal/questions/10500786-mendeleydesktop-1-13-1-fails-to-start-with-python3.
Created attachment 394286 [details] Ebuild that applies fix-python3
Created attachment 394288 [details, diff] fix-python3 patch, fixes the startup crash
Thanks for your work on this Alexander. I recently noticed it by myself (I somehow didn't received a message by bugzilla) and fixed this in the science overlay.
+*mendeleydesktop-1.13.1 (25 Jan 2015) + + 25 Jan 2015; Michael Weber <xmw@gentoo.org> + +files/mendeleydesktop-fix-python3.patch, +mendeleydesktop-1.13.1.ebuild, + -mendeleydesktop-1.12.1.ebuild, -mendeleydesktop-1.12.4.ebuild, metadata.xml: + Version bump (bug 536656, thanks Andrés Becerra Sandoval, Marius Brehler & + Alexander), changed license file (bug 536686), adding myself as co-maintainer. +