I'm in the "it's new you need to adjust" camp, except I agree completely about the top buttons on the hoods. Those things are tiny, hard to find, and you have to press directly on top of them rather firmly. Perhaps this was easier on older versions, I have Ultegra 12-speed 8170 shifters.
As for shifting, mine works great. Of course, anytime you shift from the large to small rings, there's a bit of a noise. But I don't find it any different with Di2 vs mechanical. And shifting small to big ring is a dream with Di2.
When I first starting using Di2, it didn't seem that great to me. But I used it exclusively for a month or two before I road my older bike with mechanical. That's when I realized how much nicer Di2 was. Basically, more noticeable when you lose the super fast and easy crisp shifting. I very quickly converted my old bike to Di2 after that. At this point, I don't expect I would buy another road bike without Di2.
Concerning hood shape, I think I saw a video of a pro mechanic adjusting hood fit by stuffing padding, perhaps scraps of bar tape, here and there under the hood covers to adapt the shape. It's one ting to just get used to a new shape, but another if the fit is causing pressure point issue and actual problems. If that's the case, you certainly don't' want to just live with it.