Option C, all day long. I'd go as far as to say that anyone wanting the status quo/ A/ B is in denial about how fragile and finite the paths through Manchester are.
It'd upset a small number of people but so will everything - if we are going to base the pattern of rail services in northern England on how noisy a minority of people are going to be then we'll never see any progress.
For example, I'm perfectly happy with Sheffield losing its Manchester Airport service (which it's had since the 'nineties, if not before - I can't remember) - I've used the direct train to the Airport in the past - but it's not worth the complications of reversing at Piccadilly, crossing the junctions on the flat, the "cost" of running a diesel service under the wires of the Airport branch... it'll inconvenience a few people, it may inconvenience me at some stage in the future, but it'd be better to run everything through to Liverpool - it'd make a much simpler service, it'd allow things to recover better in the event of disruption (since presumably you'd have the same TOC/ crews/ units doing both the Nottingham and Cleethorpes services). I'd be similarly okay if all of Sheffield's services swapped from "Pic" to "Vic", as long as there was no significant time penalty (which, clearly, given the single track line through Denton, there would be, but I'm not going to get precious about where in central Manchester my train stops - however I would be annoyed if the service was split between Pic/Vic - keep it all at one central station.
The same goes on other lines too - I've argued over and over again on here about it being better to simplify the mess of services - and the idea of four Preston - Bolton - Piccadilly - Airport services and four Wigan Wallgate - Victoria services is a great place to start. People know where to go in Manchester for their train home, rather than the confusion of which station to head to and hope that they get there in time.
A half hourly Chester - Calder Valley service is a similarly positive thing - not because there's huge demand to get from Runcorn to Rochdale but because you'd running from an unelectried line to an unnelectrified line using the same kind of middle distance DMUs (e.g. 158s), a half hourly service being much easier to understand and much more resilient in the event of things going wrong. Maybe if we didn't have devolution you could retain the Wales - Warrington - Manchester service as one of these trains to West Yorkshire (BR used to run services from Yorkshire to Wales), but TfW
Unfortunately , I can't see this reasonable set of proposals from happening because you just know that the reaction is going to be "by all means simplify things for other people but I don't see why *I* should have to have my services changed" from a few noisy people. But, realistically, we've got the situation where Piccadilly has the "A-list" services (to Birmingham/ London etc), which means everyone questioned in minor towns/villages are going to want *their* services to go to Pic rather than Vic, but we just don't have the capacity for that. Similarly, anyone asked "would you like your little town to have a through Airport service" then people will want it. I'd rather my cake had a cherry on top than no cherry. It's just that there's not enough capacity for everyone to have a Piccadilly service (or an Airport service/ Castlefield service etc). If your answer is "spend hundreds of millions on additional platforms at Piccadilly plus electrify dozens of miles of line" then, great, but that's not going to help things by 2022, even if you get the DIY SOS team in to try to build it all.
Give everywhere a good service into Manchester, give passengers a reliable network so that they don't need to cross reference two timetables before they know which Manchester station to head to for their train home, improve reliability by smoothing out the service patterns (e.g. rather than the situation of Piccadilly - Airport having nine trains an hour but a seventeen minute gap!) - Keep It Simple Stupid!
But, please, save me from the idea that everyone else's services should be changed in the interests of "resilience and connectivity" just so that your own favourite line can get a service to where it did when you were a lad...