fuel efficiency in these modern aircraft has been gained with swept back wings, larger intake engines etc. which with direct control and no software would be almost impossible to keep flying
discarding all of these systems because of a problem with one would set airline safety and efficiency back decades
The fly-by-wire system has multiple redundancies and layered protection, including direct law (at least for Airbus). Fly by wire is, like you say, of course a great innovation for improved control and safety, but it's nice when the plane continues flying even during a failure, however unlikely.
I guess in the case of MCAS the software was activity working against the pilots so maybe it's more of a problem with the design of this particular system and training.
The main reason they are unstable is to increase agility. Is this necessary or even wanted in passenger aviation? I don't know but I'd guess not. Probably safety, comfort and fuel economy are far more important and can (should?) be achieved with a stable airframe.