Isn't it so that Waffen-SS was under Himmler's command only at peacetime.
IIRC the W-SS was more or less acting like a contractor for the Wehrmacht: Under their operational command, but responsible itself for organisation, promotions, equipment ...
Having them under an different operational command is not possible (unless you use them only for anti-partisan and security duties). Imagine the Wehrmacht and the W-SS launching speperat offenses at the same time without mutual coordiantion or support. It would be an disaster, an amry as thin stretched as the German can't operate like this.
As for the W-SS beeing some kind of super soldiers: that is a myth (and a myth much more popular in america than in Germany).
The W-SS had a much higher percentage of tank and mechanised units than the Wehrmacht and recived new equipment before them.
But they were not more successful than similar equiped or elite Wehrmacht or Airforce (yes the airforce had a tank division) units.
What they gained in combat efficency through fanatism they lost through the lack of profesional leadership.
They only time they really did better than the Wehrmacht was during the last weeks of the war, when the Wehrmacht suffered a breakdown of leadership and moral.
To help you along with the supreme commander thing: German leadership was a mess with Hitler runing the eastern front through the army high command (OKH, he was Army commander himself since 1941) and the others through the Wehrmacht high command (OKW), while the Airforce and the Navy were more or less independent (although Hitler regulary intervented there too).
Hitler could either make Himmler SC of the Army and give him control over all fronts, make him SC of the Army only in charge of the Eastern front, or create a new Supreme commander of the Wehrmacht in charge of everything (The "Chief of the OKW" was basically Hitlers Chief of Staff and Chief Adivsor).
The last option is unlikely as Goering was very good in defending his "fiefdom".
Anybody ever becoming an strong army or supreme commander is unlikely, without a major breakdown of Hitlers health, as he considered himself an expert and meddled with every thing, regulary giving direct and very specific orders to commanders far down the chain of command.