The problem is these studios doesn't want to innovate and create new ideas for the anime industry, just profit more and more over the same shit. Just look at KyoAni and their Key adaptations, it's always the same crap and people buy like crazy.
Taking initiatives like Gainax did can be very expensive and requires intelligent and skilled people. Their staff for example is amazing, and that's why they can make visually impressive shows with low budget. And people still get butthurt when GL is praised everywhere, that's just obvious because they worked hard for it.
That's the difference between subpar studios and innovative studios.