I like the idea of separate routes, but there may be too much through riding for a complete split.
My preference would be the following:
Q94 Limited/Express: Fordham to Jamaica with stops only at Fordham Plaza, St. Barnabas, West Farms, Parkchester, Lafayette, Main St , Horace Harding, Jewel Av, Union Turnpike, Jamaica LIRR, Merrick/Archer. (If it were a subway or light rail line, where would the stations be?)
Q44 or Bx44: West Farms to Flushing, local with a few stops removed.
Q20: Enhanced service along full route, local with a few stops removed, short trips if needed south of Roosevelt.