We (Boeing) have done a lot of work over the years with regard to a generic "thrust" indication - something that would go from 0 to 100%. Short story is when it works, it's great, but the failure modes are nasty.
BTW, the reaction to Air Florida was not to get rid of EPR, it was to make the inlet probe heat automatic (e.g. JT9D on the 767, PW4000 on the 767, 747-400, and 777), RB211-524G/H (767 and 747-400) and Trent (777 and 787). Loss of inlet probe heat will automatically result in alternate (N1) mode operation.
Oh, and EPR less than 1.0 is far from meaningless (and doesn't mean negative thrust). At cruise airspeed, EPR can easily get as low as 0.7 with an engine making positive thrust due to the ram component (I don't think I've ever seen a scenario with a running engine that the fan pressure rise or ratio (FPR) wasn't positive - and that means positive thrust). Further, even if the primary exhaust pressure is the same as ambient (static) pressure, the much higher temperature of the exhaust means positive thrust.