> The App only allows a single phone to be connected now which is a problem when both me and my wife want access.

Polar opposite of our experience. We have two Nest thermostats in our home and both my wife and I can connect to and manage each one with our respective phones.

> There is also no way to run the fans without switching it on heat or cool.

Also not our experience. We can run the fans independently of heat/cool. That could be a consequence of your HVAC system opposed to the Nest itself.