Jesse,
It has never made much sense to me, but the SuperFlo VS cannot be controlled by Pentair automation. Pentair automation was designed to use the IntelliFlo style pump.
That said, even if the SuperFlo VS was capable of being controlled by Pentair automation, I would still vote for going with the larger IntelliFlo. The larger the pump, the slower it can be run and still move the same amount of water.
I say this all the time, but I run my IntelliFlo 24/7, at 1200 RPM, most of the time, for less than $20 bucks a month.
Don't worry that the IntelliFlo is a 3 HP pump.. Keep in mind that it is really a "Variable Horsepower" pump.. You just use the amount of horsepower you need for the task at hand.. Slow for skimming or running a SWCG, and faster for waterfalls or spas.
It is considered by most to be the "Gold Standard" of pool pumps..
Thanks,
Jim R.