When I search for fan controller on retail sites I just get front panel type where you can manually control the speed. Do they make some fan controllers that are simply a device you put in the computer and it revs up/down the fan based on temperature? I may be searching for wrong thing but can't find any. If not I'm thinking of just making my own with Arduino as it would not be too hard. Basically it would be a temperature controlled buck converter that goes between 6-12v or so. It would basically aim to keep the case temperature at 25C or lower and rev up/down as required, though there would be some delay to it so it's not jumping all over.
Basically it would be controlling 3 200 CFM 120mm fans. They draw 2.5a each. So not even sure if PC fan controllers would even handle that much current anyway. These bad boys:
https://www.digikey.ca/products/en?keywords=1570-1122-ND
Well, Bro -- you're a veteran member here. I'm trying to figure out if I understand what you're asking for, or that this is just a gap in your knowledge. There should be a few add-on controllers, some with their own processor, which communicate with the PC through USB to grab the temperatures from the CPU and motherboard sensors, and allow creation of "fan curves" in their proprietary software for thermally-controlled fan speeds.
One that I'm thinking of is the Aquaero line of fan controllers:
Aquaero 6
There should also be Aquaero variants that have only an internal circuit board and don't take up a front panel bay.
I still think the best solution includes selecting a motherboard with sufficient PWM and 3-pin ports, or ports that allow either PWM or voltage control of 3-pin fans. With current gen motherboards, you should be able to set the fan-curves within the BIOS and avoid installing Windows software for that purpose.
But now I see that you are using some very beefy fans -- drawing more amps than a motherboard can handle. You would have to see whether something like the Aquaero supports that kind of wattage. If not, I would hope that your fans are of the PWM variety. In that case, you could get a PWM splitter like Swiftech makes, control the fans via a PWM signal from the motherboard, and power the fans directly from the PSU.
And looking again -- Nah -- those fans are simply voltage controllable. You might want to look at some controllers by NZXT, but again, I might think it unlikely they would control fans of 12V and 2.5A.