Yeah if you're going to Liverpool you go through Runcorn and if you're heading to Warrington and/or Manchester you go through Runcorn East. Not really a case of skipping one or the other, they're different routes.
And now you mention it, it did take ages to get between stations when I walked it last year. I guess they have different markets so probably worth serving both.
I guess remaining thoughts for me are:
1) will tickets from Chester to Liverpool Lime Street/Stations be tweaked in some way. I notice there's already a more expensive "via Warrington" fare than using the "via Birkenhead" Merseyrail tickets, but I wonder if they'll introduce a third "via Runcorn" ticket or merge into an any permitted ticket
2) I wonder if there will be any local traffic between Runcorn East and Runcorn changing at Frodsham, rather than taking the bus. Depends on timetables I guess, but that could potentially be something interesting. They'd have to create a ticket for it though, as no fares exist for that journey according to brfares!!