After some experimentation with a couple of distros promising olde fashioned Gnome desktops namely Kiwi linux (based on ubuntu 12.04 and thus using an older version of Gnucash than I had been using) and SolusOS a7 (failed to boot after a slightly tricky install, well it is alpha) I reverted back to my existing ubuntu vm, which has been switched to lubuntu.
Lubuntu uses lxde which will work with vmware 3d acceleration turned off and that allows the use of Unity. lubuntu desktop also allows you to create desktop shortcuts, which means I have my custom gnucash launchers.
However it still exibits the problem I'd described in another issue: When switching between windows in Fusion unity mode the border and shadow of the original frontmost window are still visible on top of the focused window, although the window content drops behind as expected.
I'm increasingly thinking this artefact is actually a bug in Unity mode, rather than anything to do with linux per se. Just seems to happen no matter which window manager I use.