I agree that that's what everyone implicitly does, but without going into any personal details, here's how we come up on all those matters:

Permit Status:
Both spouse and I are on long-term permits working for Swiss Federal Institutions

Contract Length:
Spouse - indefinite (she's a post doc till september and then an asst. prof)
Me- At least half a decade

Ratio of rent to earnings:
We're significantly well off

Marital Status:
Young, married, strong careers. No plans of children (what the agency wanted)

Gut Feeling:
I visited them, tried being very amicable, even spoke as German as i possibly could. I really wanted this place

Now honestly, what possible reason could I be given for not getting the apartment? I'm waiting for the rejection letter...