Perhaps this has been posted before, but here is the link with explanation of taxation at the source in Geneva:
http://etat.geneve.ch/df/impots/faq....1=1554&id2=233
I heard that because of tax implications you end up financially in the same (or possibly even worse) situation, but many people still choose to live in France so it is really up to you to decide. There are different factors to consider (for example commuting time, living in urban or rural environment). I am quite sure that by choosing France you avoid the insanely frustrating process of applying and being rejected for Geneva flats.