E.R. Campbell said:
Don't blame Mr Hellyer for that. His initial plan had both MARCOM and MOBCOM with organic air groups ~ 100% command owned and operated. But times were tough in the late 1960s and Navy admirals and Army generals wanted more ships and more tanks and they, the Navy admirals and Army generals, not RCAF brass, gave short shrift to their air groups.
By the mid 1970s the air force, whose nose had been out of joint over a whole bunch of issues, convinced the CDS of the day (Dextraze) that it was impossible for anyone to do worse than the Army and Navy and so Air Command was born ~ the only time in history, as far as I know, that a major military command was organized around means of locomotion! It was an act of policy vandalism, but 100% of the blame lies with naval and military officers, none goes to Mr Hellyer and none to the civil servants who, I was told, mostly, just shook their heads, partially in silent exasperation and partially in awe of the depths of military stupidity that was on display.
I should have been more specific and say that it was "in the wake" of unification, not as consequence of it.
However, you are incorrect in stating that MARCOM or MOBCOM "owned and operated 100%" their organic air assets.
They had 100% operational command of their use - which BTW was no different than before unification - but they did not own them, they were owned and maintained by this beautiful creation MATERIEL Command, and the Navy and Army lost all control over training to that other monster: TRAINING Command.
It took the Navy 4 years to regain control over the dockyards and five to regain control over the naval part of training, even after it became clear that the Materiel/Training commands could never be made to work properly for these specialized tasks.
You may recall that, as a result of unification, the RCAF was split apart: European portion became part of that CF Europe command, Fighters became part of the "NORAD command", all transport became part of TRANSPORT command, and of course, the other assets were split between Marcom and Mobcom.
In any event, I would not say that the loss of Naval air for the RCN (or Marcom, as it was then) is in any way the result of the Admirals giving short shrift to their air group (in fact five of the nine admirals at the time were from Naval Air group). It was a result of our good friend P.E.T. cutting the operation budget by fifty percent over five years, and naval personnel by the same amount (he didn't quite do it through cuts, but by freezing the budget at a fixed amount in a time when inflation was running at 7 to 9 % a year and, at the same time increasing the pay scales of personnel ).
In any event, Naval Air (Bonnie and her air groups) represented 50% of the Navy's operations costs. The decision came down to having Bonnie all by herself on the ocean or maintaining the four escort groups we were required to have under the current NATO plans and obligations. The 24 frigates and destroyers won, for obvious reasons (in the end, even that could not be maintained, and, to artificially maintain our 24 escorts requirement towards NATO, SAINT-LAURENT, SAINT-CROIX, COLUMBIA and CHAUDIERE were put in "ready" reserve when the IRO's came into service).
But it was by no way a NAVY decision due to ignorance of the importance of naval air or of not caring for it.
As for the RCAF, the way it was split all over the place after unification, I can perfectly see why their remaining Marshals (now Generals) would have "schemed" to get some form of control over most air assets. Please recall here that, while the long range maritime air patrol assets were under operational control of the RCN at the time of unification, they were already owned and operated by the RCAF.