Yeah, me too. I've just built an all ROG system which I'm generally extremely happy with, and it's mostly living up to my high expectations. Integration of the different fan controllers and tools/utilities is one of the areas that just isn't fully living up to what I expected from it. The basics of the fan control are not bad, it's just I have a bunch of different ROG products which are not fully working as one for fan control (but do individually do an ok job of controlling the fans they are directly connected to).
The USB ROG Fan Controller that ships with the Crosshair VIII Extreme, and the Ryujin II AIO are both controlled through Armoury Crate, but the Silent/Standard/Turbo/Full buttons on the AC Dashboard don't influence them. Inside AC, I have 3 different sets of those 4 fan modes that I have to change individually on different tabs; motherboard headers, expansion card headers, and AIO expansion card headers. There doesn't seem to be any real integration between them beyond each having its own little isolated corner of AC for control.
The same goes for AiSuite & Fan Xpert, they only see the motherboard headers, none of the USB expansion card headers; and I get another set of the 4 high level mode buttons.
An all-ROG system should really have at least one tool/utility somewhere that handles all of the daily fan management and monitoring in one place. I should have a set of those 4 fan mode/profile buttons which put all of the different products into Silent/Standard/Turbo with just a single click (even if per-product individual control is retained for maximum user choice). Kinda like Aura Sync, but for fans. Also, it would be kinda nice if the software recognised that a high end system is quite likely to not have a CPU fan or anything connected to that particular fan header; I'd love to get rid of the prominent mentions of CPU fan and "0 RPM" in danger-red next to it on the various panels that show fan information, replacing it with something useful such as the AIO or chassis fans (which may not all be on the chassis fan headers in the case of ROG motherboards that ship with a fan expansion card).
The last thing on my list of fan irritations is the front panel and little fan speed card in the Helios case. That really needs an update for such a premium and beautiful case, to add some sort of motherboard fan speed control for the case fans. The basic high/low manual mode button on the front panel is ok for lower and mid range systems, I guess, but it would be fantastic if there was a way to integrate it cleanly on the high end. Maybe the button could have 3 modes, like the front panel lighting button (where the 3rd mode is motherboard control)? Or, have an optional USB-connected board which can replace the basic case fan controller and turn the button into swapping between Standard and Turbo in AC / Fan Xpert? This is more of a "nice to have" type thing than the issues with the various different software controls not integrating fully, but it would be something to really reward customers who do build the all-ROG high end system (little details like that can really help to keep the brand reputation and premium status).