I know you're currently going through the process of purchasing a new 40-foot fleet. Here's the thing. I don't really much care what sort of buses you buy (as long as they're partial-low-floor, CNG, and have those nice amber headsigns, but you've already got that much down, so...), but I really, intensely care about what you put on the front of them.
Specifically, the new buses need three-bike racks. More specifically, I'd prefer it if you installed the Sportworks DL-3 "trilogy" bike rack on every bus in the fleet. These seem to be the only three-bike racks out there that also support the bike's rear wheel, making it less likely that a bicycle will fall off the bus. (This is a serious consideration for those of us who ride with panniers and rear racks, especially when said racks are loaded.) They also don't seem to have the complicated problems of other three-position rack designs, which Seattle's King County Metro seems to be dealing with at the moment. (See the bottom of that post.)
So, RTA, do the right thing for those of us who choose the independence of the transit/bike combo. Buy three-position bike racks for the new fleet.