Interesting proposals, the standardisation of the timetable will no doubt help with crew and stock diagramming, and also with all trains along each route going the same place should make understanding the timetable easier, even if it means that more passengers will have to change trains than do at the moment. West Coastway is one of those that you can either make complicated by having trains from "everywhere to everywhere", or a regular set of services on the same flows with decent connections, as proposed here.
Had Barnham been a full twin island station then this could have been ideal for double connections on this route, but with the layout as it is then connections will be longer.
The biggest issue that I see is the two services terminating at Chichester, which could create a new performance risk. Dwell times for arrivals and departures will need to be fairly slick, plus with crossing to the up side siding to reverse, any delays could be passed onto the through trains. Coupled to this, although they are quieter stations, one could expect noise from users of those stations West of Chichester which will see the "skip stop" pattern. It would cost another diagram, but maybe both could be solved by the Class 2 services at this end of the network staying as now, with one of the trains coming out of Littlehampton (now Brighton) going to Portsmouth & Southsea calling all stations, while the other goes to Bognor Regis as one of the branch shuttles, which would also maintain the status quo from Littlehampton westwards.