Um, why do the Aether Foundation employees make people think they're villain grunts? Every professional job has a uniform, and this is theirs.
While from a real-life perspective this makes sense, in the pokemon universe only villainous teams have uniformed employees. While there are plenty of examples of shared trainer sprites/models, none of them seem to be unique to specific organizations (unless you want to argue that Boss Joey is enforcing an all-shorts dress code on the other youngsters. On an unrelated note, I have a new favorite headcanon). The key thing is that the shared sprites of the villainous organizations are
explicitly the uniforms of a specific organization. Other NPC's with shared sprites don't have any established relationship to each other. Even for police officers, it's not clear whether they all belong to the same precinct or what level of organization between them exists. We never see a police chief, nor any organized action by officers against villainous teams (angry old men tend to be more effectual). When it comes to large organizations, villainous teams are pretty much the only ones that exist in the pokemon world.
Moreover, there are a lot of other factors in favor of them being villainous teams. One of the huge clues is that the Aether Foundation plays heavily into the Promethean themes that have strongly influenced the pokemon series. Starting with Mewtwo, the series has always had the warning of the dangers of meddling with the natural order. The artificial island and mission statement of the Aether Foundation plays heavily into that theme. There's also the subtle word choice of using "experiments" instead of "research". Pay careful attention throughout the series: the pokemon professors do research, the evil organizations perform experiments. In the real world this would again be a stupid non-distinction, but in the pokemon universe "experiments" imply some kind of unnatural interference and therefor tend to be much more suspect. This is more subtle and subjective, but the Aether Foundation hews closely to themes associated with villains in the pokemon universe.
Another issue is that we haven't actually seen very many large organizations with a clearly-defined hierarchy in the pokemon world. Forget uniforms and sprites, let's just look at the organizations themselves. Setting aside villainous teams, we've seen Silph Co, Devon Co, and... maybe Lysandre Labs if you want to count that separately from Team Flare? The pokemon league doesn't seem to actually have any central authority, there's little evidence of a central government, and what few police officers we see don't seem to be part of any larger force and we've never seen a police chief or any indication of some kind of leadership or command hierarchy. The point is, the pokemon universe seems to have exactly two kinds of large organization: passive mega corporations that never do anything proactive in the story, and villainous teams. Once again, Aether clearly isn't going to be a passive part of the story and fits much more nicely on the villainous team side of the spectrum.
Next up we have the rather distinct choice of words for Lusamine's introduction: "Even pokemon from distant worlds, far from the Alola region, are worthy of my love". You can sense the hubris dripping off that comment, and it seems likely to be setting up the villain for her downfall. It's similar, if a tad more subtle, than Lysandre's introduction with Diantha in XY. Lusamine seems a bit more subtle than Lysandre in terms of the "villain vibe", but not by much. However, I wouldn't say that's definitive since Zinnia was even worse than this and she never got her comeuppance. Still, Lusamine seems much closer to the arrogant introduction of Lysandre than the mercurial introduction of Zinnia (who only became insufferable later on, and I'd attribute that more to bad writing than the intent of the writers) and I'd be much more inclined to draw the comparison between Lusamine and Lysandre which supports the villain conclusion.
Finally - and this is probably just wishful thinking on my part - but we are LONG overdue for a female antagonist lead and Lusamine fits the bill perfectly.
TL;DR None of this is certain, but virtually everything we currently know about the Aether Foundation is consistent with them being an antagonist in the pokemon series. It could be a cunning misdirection to play against the expectations of older fans, or maybe we're all reading
way too deep into this stuff as we often do. Until we get confirmation one way or another I'm certain this fan theory will persist, and a lot of people are going to feel very strongly that
Team Aether Foundation are actually villains.