The cause of this behaviour is targets, more especially the Public Performance Measure. Even if the branch service is run by the same franchise as the main line it's connecting out of, a delay to the branch train still goes against the PPM, and if that then causes a delay to another train (as might happen to the above FGW service at Guildford) compensation has to be paid. All part of our disfunctional franchise system.
I was at a recent consultation held by the Welsh Assembly at which it was suggested that customer satisfaction would be a better measure of franchise performance than PPM.
How late does a train have to be before they pay out? Is it after 1 minute or 5 minutes?
As someone who tends to end up travelling to places via connecting routes that are less popular, I know what connections can be like. 20 minute wait at Clapham Junction or rushing through central London via underground because London Midland were late once again. Missing a connection would add 20 minutes onto a journey.
I tend to think railways are now run for people to get from A to B but not A to B to C.
I do think time is important. From Guildford, it is quicker to drive to Ash Green or any other station beyond Aldershot as the train waits 10 minutes at Aldershot. Again officially the train from Aldershot to Farnham leaves 3 mins after the Ascot bound train gets in from Guildford. Anyone looking online won't know the trains use the same island and unofficially you are most likely to make your connection. Thus they might drive.
Going to Portsmouth from Guildford in the morning peak is slow because every train stops at every station. I think the 8.04 is the first fast train, 7.25 not getting in that much earlier either. I don't know if factors like this play a part in people's travel plans.
If any of the above situations is replicated across the country it might explain some station usage stats and route usage stats.