I think the overall point here is that CSS3 is only great for simple animations. And most "websites" can take easily advantage of simple animations with transitions to do boring things like fade a tooltip or animate a menu dropdown or accordion. That is the extent of what the vast majority of "websites" do, and CSS3 is perfect for that (and I even like having that logic in CSS). However when a site becomes more of an experience, with interactivity and life, CSS is pushed way past its limit. I think people get caught up in imagining using GSAP for regular ol' websitey stuff, and I don't think that's its goal. Just because something is animated, doesn't mean its animation.
I have just recently used GSAP in my first project after finding that transitions could not easily do what I wanted in that case. I used about 5% of GSAPs features and it was so perfect for me.
I hate to say the same thing that I've read a thousand times, but let the project drive the technology.