What will you do if you don't like the way a tier looks in the future? Say Donphan does make it back to OU under 1760, what do we do then? Because it is pretty clear that the point of this is to make OU look the way you want it to, will this system be modified further in the future to make the tier look the way you want it to?
People will always have their own personal tiering opinions. However, that does not mean they will suggest for a change just because they disagree with a few things. We feel as if the current tiers do not accurately represent the metagame at all. That is why we are suggesting change. We aren't suggest changing because "lol Donphan is OU, Trevenant is OU, and so on and so forth"; we are suggesting change because there are so many Pokemon displaced. (this is subjective; yet there is a large enough displacement that a lot of people agree that there is a problem) People won't seriously suggest change until they feel the tiers are very inaccurate. Regarding your point (paraphrasing) "we didn't do this in BW when people had a problem - why start now"... because even though people had issues with the Pokemon in the tier, not many people felt it was enough of a problem to warrant change like this. In addition, we DID do something about it: it was when we first implemented weighted stats in the first place. Anyways, now people feel as if there is a problem with the stats, which is why they are suggesting change.
I emphasize - we're not proposing this change because Donphan is OU and Latias is not; we're proposing the change because there are so many Pokemon displaced that the tiers are not representing what is actually good in the tier. This may not be the central goal of tiers, but it is certainly an important attribute in them.
Lady Salamence, this is very similar to how we do suspect tests (and for the record, these account for even less users). You can always have influence on tiering, as long as you are willing to put in the time and are good enough. It may seem "elitist", but in the end, we are the lead in our tiering system and... again... you can still affect usage stats as long as you put in the time and are good enough... which should be a goal in a competitive Pokemon community. Tiers should accurately represent (for the most part, of course people will have their personal opinions) what is good in the metagame.
I think you bring up a good point - whatever we go with, the exact Glicko number should not be announced, so it's harder to take advantage of. We can of course agree on exact % we want (which is still up for discussion), but whatever Glicko number that ends up being should not be revealed. While we're on that topic, it's not as easy to take advantage of as you think. For one, the top 2% of the ladder is still a huge number. Even if one person decides to spam something like say Suicune in OU, they're still only 1 person. Plus, if a Suicune is getting them that high on the ladder... isn't it worth some consideration at least? And while you could bring up people like ShakeItUp who manage to get really high with stuff like Mighteyna in OU... the amount of people that can and are willing to do that is much smaller in comparison to people playing "legitimately" is very small.
The exact % is still up for discussion. The top 2% may seem very restricting, but in a huge ladder like OU, it still accounts for a lot of people. Of course, we can still change the numbers if people feel as if it's too restricting still. UU and RU do not need to use the exact % as OU either - it can be modified to account for more people if it would be benefical.
In essence, even if this solution may seem arbitrary and elitist, in the end, if it makes our tiers look a lot "better" (again this is subjective... but a lot of people agree there is a problem... and it's clear that taking stats from "better" ranked people on the ladder improves our tiers) then as DJD stated, the tradeoff is worth it.