Just to clarify - are these feeds for a single agency/brand "Foothill Transit" that is presented to the rider? In other words, if you populate agencies.txt in two static GTFS datasets will the records be identical? Or is more than one agency/brand presented to the rider (e.g., one per CAD/AVL)?
I agree that having a single GTFS and corresponding single GTFS-realtime feed is ideal and should be supported by all consumers, but it sounds like you'd need to build a GTFS-realtime feed aggregator to do this (an aside - I don't know of any out-of-the-box open-source tools that aggregate GTFS-realtime feeds, but in theory it wouldn't be too hard to create one based on some of the demos/utilities listed here
Outside of that, if you're stuck with two GTFS-realtime feeds it will depend on individual consumers if they prefer/support a single static feed or two static feeds that each correspond to a GTFS-realtime feed. If both CAD/AVLs are for a single branded "Foothill Transit" agency, I would think the single static feed would be preferable - otherwise, if the same agency is split across two static feeds the consumer would need some way for you to map that data together so they don't appear as two separate (but duplicate) agencies in the consumers UI. To my knowledge there isn't a standardized process for declaring that two agencies in separate static GTFS files are the same logical entity.
It would be great if consumers could comment which they support/prefer.
Center for Urban Transportation Research
University of South Florida