There are no problems regarding Switzerland not being a member of the European Union as every EU carrier could operate between Switzerland and any other EU country without restrictions. Switzerland became part of the EU open skies on June 1.
As mentioned earlier, Zurich is not very attractive for low-cost airlines. The airport is not only very expensive but also quite congested. At the moment, with all the construction work taking place, it takes up to eight minutes to get to the parking position after landing on runway 14 which is used on most landings. Not very popular with low-cost airlines. easyJet, which is the biggest LCC at ZRH, is reportedly not interested in expanding operations there because they are very unhappy with the general situation at the airport.
Geneva is an easyJet base and therefore let's say not very attractive for other low cost carriers. easyJet is obviously willing to fight against new entrants. They announced a new flight between Geneva and East Midlands just a few days after bmibaby announced to launch a daily flight on this route. MyTravel Lite, the other low-cost carrier operating into GVA, is also competing against those two airlines operating flights between EMA and GVA instead of BHX and GVA. Virgin Express is the only LCC operating to GVA which was not attacked by easyJet, most probably because easyJet didn't have an operation at BRU yet.
The only airport I could immagine to become a base of other LCCs is Basle/Mulhouse, the airport just build a new terminal, but Swiss is slowly pulling out of BSL and I wouldn't be surprised if they would cut the regional hub there. So the airport is looking for new carriers to start flights to BSL. There are rumours about Air Berlin considering starting flights from BSL to Barcelona and Rome Ciampino, however I am not very optimistic this will ever come true.
Swiss aviation news junkie living all over the place