Historically, Geneva and Zurich had always worked with different systems and sector layouts, and Geneva was always more advanced, mostly because Zurich failed to be as innovative.
What is happening now in Zurich regarding system compatibility is a mere catching up to Geneva level, nothing more, nothing less. Of course the system being in use in Geneva can't be adapted on a one to one basis, as those different working philosophies can't be overcome from today to tomorrow, but the end result will be as close as it can get.
It may be interesting to know that for instance in Langen ACC, Frankfurt and Düsseldorf sectors are located in the same room, but their systems can't "communicate"!
On the other hand, the above does not apply to APP/DEP, where, IMHO, Geneva is lagging behind. CALM has been in use in Zurich for several years and it has made life a lot easier. Now that Geneva APP are about to introduce an electronic coordination tool as well, they, to my knowledge, do not adapt CALM, but they intend to reinvent the wheel by setting up their own system. So much for "one operation"...