The problem with that "rock-paper-scissors" viewpoint... is that it assumes that everything has a 'perfect' counter to everything else.
And - arguably - sniper com does have its counter.
Albeit far from perfect.
That which is T2 Point Defense.
However, spending 800 mass on your own gun upgrade isn't worth it, as you're outranged, regardless;
So, you're forced to take the T2 route instead - and, on top of that, it's about 540 mass for a T2 PD.
But, we all know one T2 PD, two, or even three won't stop a rampaging Sniper Com.
The issue here is that the 'counter' isn't as effective as it may appear to be.
An Aurora is a far better example of a more balanced unit as it has half HP for the extra range it has.
The same can't be said about the ACU - there is no 'con' to this huge 'pro' it has.
In fact, most, if not all, units that have superb range, they all have low HP. Auroras, Sniperbots, Fatboys, etc.
But the extra range isn't just worth 200 mass - it also denies everything any other com can do or try to do.
Which is worth far more than can be put into mass values.
Another note here - which I have mentioned in a previous post above ^, is that the counter to something should be cheaper, at most the same value. However, this isn't the case for an Aeon sniper com.
There is also the case as to why Aeon Navy got nerfed with the last balance patch, too - but that's a slightly different story.
To put it blatantly. Rock counter scissors as well as paper - hence, leaving very little room for a proper counterplay from any of the 3 other factions.
That being said... I completely agree, we don't want all units to be the same, otherwise, we will end up with just reskins, as you mentioned.
But, should an Aeon sniper com's range be THAT high?
No, it really shouldn't.
~ Stryker