Now for some comments from your resident transitologist. Mixed feelings about this one. A unified MARC/VRE brand would be helpful to those whose travel needs include getting from the Virginia side of the Washington metropolitan area to the Maryland side, or vice versa. It would MAYBE eliminate the need to change trains in Washington with the associated wait time in between. The downside to this is that your origin and destination would have to be along the same married pair of routes, or there would still be a change of vehicle en route. I believe this is why SEPTA's marriage of ex-PRR and ex-RDG routes into "R" prefix routes in 1984 seemed like a good idea at the time, but ultimately by 2010 did not work out. Most people still had to change trains at one of three downtown stations.
In the case of equipment use, the pro of through service would be continued utilization of the trains, vs storing them at or near Washington Union Station. The through tracks leading to/from Virginia would see more use, and those that terminate at the bumper from the north would see less use by commuter trains. It should, at any rate, make more track slots available since tracks won't be used as much for storage.
Integration of fare models into a unified system would be a challenge, but not impossible given today's technology. Some sort of tap on-tap off system similar to other commuter railroads and transit lines could work as it would simply register the passenger's boarding and detraining location, no matter on which section of the system.
A question that burns in my mind is, where in this megalopolis does it stop? Besides this discussion about merging MARC and VRE, there has also been talk in other threads here about bringing MARC and SEPTA together, likely at Newark, DE. And then SEPTA touches NJ TRANSIT at Trenton, and in New York City, NJ TRANSIT meets LIRR (and maybe Metro North someday with service extended into Penn Station off the Hudson and New Haven Lines). I could continue right up the east coast to Massachusetts with current or future commuter rail properties meeting one another and possibly requiring fares to be integrated. This is not to say that someone would get on a train in Spotsylvania, VA and travel solely by commuter rail up to Haverhill, MA (also assuming a North-South Stations tunnel in Boston) because it would obviously take too long, but if we're going to discuss the integration of fares between two systems, then the number could be endless even if there are still multiple physical transfers required.
