To some degree, I agree with you. A lot of fans have been jumping to conclusions and expecting Game Freak to give them what they want and give it to them now. But as far as the negative reception in general, if the type of game they wanted has already been ruled out and they have no interest in a third version of Alola, why shouldn't they be negative about it? You don't expect people to just roll over and accept whatever **** Game Freak plops in their lap? This market works by developers making a game that's actually desirable that people want to buy, so if they're not meeting the fans' expectations they shouldn't be buying it.
And frankly, Game Freak had this coming. This is what happens when you take "uniqueness" to a ridiculous extreme, when you have no guarantee of quality or that any of the elements you enjoy about the series will carry over to the next game, negativity and lack of interest is a natural consequence. Wouldn't be surprised at all if that also translates into lack of sales and this game ends up being the worst selling main game of all time.
You say people are a little justified in their anger because the game they wanted has been ruled out but if people wanted a third version of Alola, they're getting it, they wanted a game that expanded on the role of Necrozma and that's exactly what US/UM is (from teaser stuff anyway). What more do they want, is it just the "Stars" brand that they wanted, did they want a basic "third version" of the game instead of something a bit different or is it something else entirely because I can't understand the anger from people who wanted Stars, at least not completely.
You then have the people who wanted Gen IV remakes and I'm sorry but I find those people to be amazingly delusional when it comes to that. The gap between HS/SS and OR/AS was 5 years and 2 generations and now people want the next set of remakes to come out only 3 years after the previous one and in the next generation no less; at least FR/LG being Gen 3, it still took 7 years until we get HG/SS so to not only anticipate but to demand that we get Gen IV remakes only 3 years after the last set of remakes is kind of pushing it. Again, I do believe they're coming but I still think it'll be Gen VIII (it goes along with the numerical theming since you had 1-3, 2-4 and 3-6 so 4-8 makes a bit more sense).
I don't think fans should just accept whatever GF puts out or say it's amazing (I myself have issues with Black/White as well as Sun/Moon for being too story heavy and too linear) but I don't think this level of hate is deserving for these games, they're just the third version of Alola but with a slight spin on it. You don't have to like them but I don't think this negativity is, as you call it, a natural consequence. As you mention, people get worried if they fear certain elements of a previous game won't carry over to the next one but hasn't one of the major criticisms of the Pokemon games been that they're too formula-based, at least when it comes to game mechanics; the fighting's the same, the plots are generally the same, the goals are the same (collect a number of "badges", become champion) so unless people are worried about the more game-specific elements, like changing your appearance or Pokemon following you around (which I will never, ever understand why that's such a big thing with people, I don't get why people act as if that one feature is an absolute must) then I don't think they have much to worry about. Ultra Sun and Ultra Moon will play just like every other Pokemon game before it with slight differences and almost nothing removed from Sun/Moon (because the assets are already there, why remove them). Pokemon has basically been the same game for 21 years and still it has a large fanbase, it still has a large adult fanbase who started with Red/Blue so I don't get why this game is the tipping point, it's nothing we haven't seen before so what makes it special, what seperates this game from Platinum or Emerald or Crystal that is making the fans claim this is where they draw the line. If they fear change, then why worry when you've been given no reason to assume great change and if they fear more of the same then again, I go back to my previous question.
I feel part of the problem is this mentality of "It was ok then but not now", you see it with how people react to new Pokemon and how the designs look uninspired but when anyone brings up the simplicity of older designs, you get the line of "It was ok back then but now they should have higher standards" even though we're nearing 1,000 Pokemon and for the most part, they've made all of them look fairly unique and kind of cool (excluding your mainstays like the Pikachu look-alike) and so I think that people are more forgiving of "third versions" from the past because that was the past but now they should be doing something bigger and better even though we're now at a point where alternate universes are a thing, story is getting more focus (I'd say a bit too much focus) and I personally feel that the series has matured in some aspects but I guess in some cases, people only look at the surface level and that's it.
I don't think Pokemon has a problem with being overly unique, I mean, it's not like Final Fantasy where they overhaul the entire thing for every new numbered entry, I think the problem is something of the reverse, it settled into a formula (from a release standpoint, you get the 2 base games, a third improved version and in some cases, a remake) and so after 4 generations of that, people became accustomed to that and so GF tried shaking things up a bit and to be honest, you can kind of see it begin with Gen V because maybe it's just me but I always feel it acted like a new cycle, a new generation. You had the world and standards of the first four generations and then everything changes with Gen V, they begin again and they do new things, they don't give you basic third versions, they give you sequels, they might not do the third version at all or they do whatever US/UM will be because I guess there are some formulas that even the developers get tired of. So I don't think they're being "unique" for the sake of it, I think this is them trying to work things out, see which ideas work and which ones don't, should they go in a more story-based direction or keep the traditional adventure aesthetic and should the generations connect together in a greater sense rather than just a few quick cameos. I will admit that maybe US/UM is more of a growing pain period since I feel they are the culmination of 2 generations creating one long narrative (the one of alternate dimensions and the idea of "Fallers") but purely from a business standpoint, they're not doing anything overly risky and they're not doing anything different, it's just a group of fans being entitled and believing they're being denied what they feel is owed to them.
I'm not saying you have to enjoy it simply because you enjoyed the previous games but I don't think you should attack it for not being what you wanted and if it's not what you want then you're not expected to buy it, Pokemon tends to be a yearly thing now, maybe you'll enjoy what they release next year.