Prune Hill is probably the least useful to bridge - it was low enough risk that it was still an AHB until last year. When I worked in the area, I only used Prune Hill if I had was working at Royal Holloway.What I don't get is why the council don't build a bridge at the Prune Hill crossing adjacent to Royal Holloway UoL or apply for funding for one? There's plenty of land, and it would lessen the queues at the other 2 level crossings.
It also doesn't get you to the most useful of places. The main problem crossings are Pooley Green and Thorpe Road with people from Egham Hythe making for Egham and Staines town centres. Egham station is less of a problem. I used it a few times at the same time I'd have been hitting Pooley Green and the queues were less.
I suspect that the crossings cannot be fixed from the road side, and the only one that could be fixed from the rail side is Thorpe Road, but that would be ruinously expensive (I am guessing it would require raising the railway from Staines Bridge getting back to ground level near Pooley Green.