I think a big part of the price difference between the two companies was who does the work. Sunrun, as it turns out, contracts through other companies to perform the installation. The company I spoke with last night (Solar Energy World) does all their work, so there's less overhead. They're also a local company, which I think helps.
The design of the system was a factor, too. The first design had panels on both sides of the roof- the north side and the south side. He told me that was because they had a minimum system size. However, the second guy ran his calculations and showed me he could hit 86% of the same output by putting panels on just the south-facing roof. So, yes, the system will be smaller in terms of # of panels, but they're putting them where they will actually make sense, instead of blanketing both sides of the roof with them- and getting very little power from the north side, especially in the winter.
They use a more intelligent inverter system too, which optimizes energy production on a per panel basis (not micro-inverters, but a setup that allows the large inverter to work in a similar way).
The panels themselves are slightly more efficient, and also meet the criteria for U.S. made content, which actually makes them cheaper due to the import tax structure for "green" energy components.
Combine it all up, and my out of pocket cost for the system will end up being less than $2 per watt, after federal and state incentives, and even less due to these "Solar Credits"- basically, an extra credit on the bill (on top of the net metering) for "green" energy production. The SEW rep explained what I had heard about Net Metering sunsetting too- basically it's the limitations of the grid to absorb surplus solar energy, and how it varies region by region within the state. Since we're in a rural area with few solar installations, there's no risk of that happening here soon, and if it does, it only prevents additional customers from coming on, until new transformers are added.
On top of all_that_, SEW was able to get me a full point cheaper on the financing, which saved on the monthly payment as well as the interest costs over the life of the loan. Basically, the monthly payment will be approximately what I had been paying BG&E for electricity. When the loan's over in 12 years, I own the equipment, and all the power it generates.