I don't think thats what happened at all. I mean look at Sonic AM, that was MUCH darker then Reboot and ran side by side with Reboot.
Keep in mind, Reboot was Mainframes FIRST series. Mainframe (the company of course) has an amazing back story of how they got started. Even though they had LOTS of talent, very few actually finished any kind of college.
It took Mainframe some time to sort out internally what kind of stories they wanted to tell, who was best at telling them and what got ratings. Overall, they really didn't do a bad job timewise in figuring that out and it didn't take them long to pump out some really good action series.
Let's face it, Mainframe was perpetually one of the best animation studios on North American soil in the 90s. Save all the story issues they had with Beast Machines, I think everything else they pumped out was an instant classic. I only hope we get the same quality out of Dream Maker when we see their rebooted Reboot next year.
Flintstones / Jetstones are series I don't think aged really well. I don't mind watching them and their transition is certainly much better then many things of its time (and even some in the 90s) but I defiantly think the humor is largely disconnected to anyone who grew up later then the 80s. The graphics and to a lesser extent the BGM both haven't aged well at all.
I tend to think Flintstone Kids aged a lot better then Flintstones at this point. I'm not so sure it will hold up in a few more years though.
Hannabarbera did most of the Super Friends / Super Powers series. I'm not sure if someone else did these "Lost episodes", but I'd wager it was HB.