I have a feeling we'll all get used to the new Pokemon looking like "terrible fan made creations" soon enough. Personally, I've felt that way about a number of Pokemon for the past couple of generations (a bunch of the gen 5 and 6 starters, as well as some others), and I've definitely heard similar complaints from others. Yet in the end, I've come around. While most of those Pokemon still aren't my favorites, I like them better than I did to begin with, and they look less out-of-place than they did before. That being said, I generally still prefer the Pokemon from the first couple of generations. But there are some "normal" looking Pokemon in the mix this time to offset some of the stranger designs, and I think that'll help.
The changing mechanics, though still strike me as a potentially big issue. While there have been some changes mechanical changes that I hated the sound of but came to love (the physical/special split particularly stands out), there have been other changes I haven't cared for (e.g., mega evolutions. I use them, but I still don't like them very much, and I still think the series would be better without them). Eliminating gyms strikes me as a major change, and I'm worried that it will change the gameplay too drastically. (Not that gyms really matter that much in the long run, as I spend hardly any of my game time actually clearing them, but still...)
Maybe some of this is my frustration with [in my view] Nintendo/Intelligent Systems' killing of the Paper Mario series by turning it into something different than it was before, but I'm afraid that the changes seen this generation could mark a shift in the Pokemon series that will ultimately make it unrecognizable. I have a feeling I'm wrong about that, as GF seems to have a better grasp on what elements make up the core of their series than IS does, but still, it is a fear. And in a year where I personally have seen a lot of creators of series (games, books, movies) from my childhood take steps in directions I don't like, I suppose I'm a little more eager than normal to avoid significant changes in the Pokemon series and maintain the status quo, with small improvements here and there.