I do have 2 phones recognized in the system. What I do find is, when the car starts up, it takes a little longer for the system to "read through" and find whichever phone is active and it wants to engage with at the time. When it doesn't find the first phone, it does auto-engage with the second. Admittedly, a little kluge, but does seem to work. Where your system may be getting stuck is... if you and your wife are both in the car at the same time and the system is trying to engage with both active phones. I have never found a "this is default phone" setting in the system, but then again... the subie software is not known for being all that great.
You might try figuring out which of the two of you drive the car the most. Then sync that phone in to the system first. Then, add the next person/phone. This might at least get the system to put the most often used phone in 1st place of the system, so at start up, it finds that phone and engages first. Not a great solution, but maybe a work around.