Why would you need to rebuild Levenshulme or Heaton Chapel if you switched to pair by use?
The stations still end up with one up and one down platform.
I admit it would be a bit odd that the northbound trains don't come from the same place the southbound trains go, but the two top destinations from Levenshulme are Manchester Piccadilly and Stockport.... and no other destination is even above 5000 per year.
EDIT: Heaton Chapel has ~71% of its traffic being from Manchester Piccadilly or Stockport and 63% for Levenshulme.
The remaining passengers would have to change once on a round trip, but after a rebuild half of them would have to change twice on a round trip, so I don't think improves anything.
To summarise, I suggest a change to paired by use/destination and assigning northbound/southbound calls at the intermediate stations to whichever train is available on the relevant track.