I think people are still wary of the extra force org because there are a lot of cheesy things you can do with it. What people fail to realize, I think, is that the second force org chart comes with an innate massive cost that severely cripples your ability to spam, and that is namely that you must take a second HQ and two additional troops choices. If for some reason you were running two HQs and four Troops anyway that isn't a big deal, but even in 2k games most people will take, MAYBE two, HQs, and up to three troops. Taking a marshmallow HQ/minimum squad size Troops choice just makes them easy victory points, especially in 2K where you can expect a few blast templates, massive torrents, and soul-crushing assaults a turn. To get that extra psyflenaut/doom scythe/basilisk/trygon/whatever, you must make a massive initial investment into something you may not have actually even wanted.
People will get used to the double FOC, and realize its basically just mini-apocalypse without all the crazy fucked up rules and titans.