I like this idea of shortening the really long routes a bit.
I'm thinking terminating the M101 at 125th St/1st Ave where the M100 ends is pretty good.
The M2 and M4 both could be truncated to 96th St/Madison Ave (except late nights for the M2)
install a new route (M13) making all local stops on 5th/Madison Avs between 8th St & 106th St, route will replace M106 along 106th St and terminate at 106th St/FDR Drive
keep the M3 and add full time limited service except for late nights.
extend M5 back to Houston St like the pre 2010 days
renumber M55 back to M6 and install a new southbound route via 7th Ave, 32nd St, broadway
extend the M1 back to South Ferry just like the pre 2010 days, also revert back to Park Ave south of 40th St
extend M10 and M104 down to Penn Sta, terminating at 31st St.
increase frequencies on the M102 and M103 as they are now the only two Lex/3rd Avs routes. Also implement Limited service on the M102
with the M106 eliminated, more resources will be used for the M96 and the new M13.
M98 extended back down to 34th St.
this is all for better Manhattan service