In general, just because a manufacturer does not produce a product that you desire, it does not mean that they have "an issue" with something. Your needs or preferences (while perfectly reasonable) may not be at the center of their target market, or may not represent something that has a sufficient ROI to warrant an investment.
Subaru's EyeSight is a leader in driver assist systems in non-luxury class cars. The two key features in driver assist systems that seem to be driving the market are ACC and Forward Collision Braking (or whatever various people call that feature). And Subaru has done a great job with both.
Yes, there is more to driver assist features than ACC. You know that and I know that. But MOST people don't see past the ACC. (Just read the comments of people on various Subaru owners forums like this one, and you'll see that most people use the terms EyeSight and ACC interchangeably.) So whereas YOU don't think ACC is EyeSight's most useful feature, the market as a whole almost certainly does. The good guess is that Subaru wants to address the broader market. It's always the case that there will be individuals such as yourself who want something different than the broader market.
Making ACC and FCB work in a manual is not easy. ACC you can't really do at all unless you're willing to limit its value to varying the speed over a small range of speeds. Better than nothing, I suppose, but not really "ready for prime time".
Subaru mainly sells automatics/CVTs. To justify a special version of the EyeSight technology for manuals, there has to be a business there. And the typical buyer of a manual is more of the "purist" kind of driver, i.e., the type who would be less likely than the typical automatic/CVT buyer to want a nifty automated system like EyeSight.
Maybe if at some point Subaru sees their sales of WRXs and STIs being hurt by the absence of the availability of EyeSight, they will start worrying about it. (Although given that WRX sales for April 2016 represented a 14.1% year-over-year increase, I don't think that will happen any time soon.)