It’s an interesting idea, but ultimately one that I doubt will come to pass. Specializing engineers into their own branch (and make no mistake, this will not be a separation of equals) may yield some improvement in the operation of the engineering department, but it is unlikely to improve ship handling or combat performance.
On the other hand, specialization will damage the Surface Warfare Officer community. That may not sound important, but it is. On all but the largest ships Chief Engineers are first or second tour department heads (LT or LCDR). Unless Big Navy is willing to create scores of CDR billets, engineers will not have a viable career path that parallels their topsider cousins. As the Navy found out with its last attempt at creating SWO specialists, no career path means no interest.
As the “mainline” SWO community spins off the engineers, it will grow smaller, and have less of a voice at the table for allocation of resources. While you may be right in pointing out that community clout is a poor way to run a railroad, it doesn’t change the fact that SWO is best served by putting up the largest numbers they can.
Finally, there is benefit to having jacks of all trades. Right now to be eligible for command it is not necessary to have done an engineering tour, but it is necessary to be qualified EOOW (OICEW). Understanding how the plant operates (theoretically) makes SWOs better ship drivers, because they know her capabilities and limitations. It may not be strictly necessary to know how a power train works to drive a car, but it helps. More importantly, knowing what the plant can and cannot do is tactically relevant in combat, when limitations of 60hz, 400hz, firemain, seawater, chilled water, LP air, etc. influence what and how you use your weapons systems.