Both cities and their surroundings have plenty of good places to live so that shouldn't be an issue. You can even live somewhere equidistant (eg Northwich) to give your career maximum flexibility in the future.
As a pilot, do you want to do ILS after ILS because it's too busy for anything else (Manchester), or have fun and do loads of visual approaches (Liverpool)?
Do you want to have to take a bus from the staff carpark (Manchester), or just walk to the terminal (Liverpool)?
(Assuming of course that your car is still there when you get back)
Liverpool is getting busier but it still doesn't suffer big airport syndrome.