What Mainly Determines Rent Rate?

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I know that many factors can contribute to what you're able to charge for rent: comparable rents in the area, condition of property, number of bedrooms, square footage, etc.  It is all very local.

My question here is a general one though.  What determines rental rate more, square footage or number of bedrooms?

I'm in the planning stages of building a duplex.  I'm looking at one design that is 1200 sq ft and 3/2 per unit.  The second one is 900 sq ft and 3/1 per unit.  Obviously the second one will be cheaper to build, but which will ultimately be more profitable?  That's what I'm in the process of figuring out. 

Again, I am working on getting solid estimates based on comps, but in the meantime please give me your thoughts on this generally.