I reckon most of the whingeing about Roddenberry is about 'Gene's Vision' so it is story related. It's like he is undeserving for how the franchise developed and how he held things back.
Nope. The people who seriously whinge about Gene's Vision are typically attacking everyone who came after him for not doing things exactly like he would.
When people who are criticizing him bring up 'Gene's Vision' the context, ime, is almost always about how his personal actions so often ran completely counter to the principles he claimed to champion in his work.