and yet.... it shouldn't be.
Precisely!
And why, pray tell, it shouldn't? You never saw a tank firing it's main gun at the helicopter IRL, aren't you? That's what AA systems for.

Here we have the same situation. MWLL is a combined arms game, set in BT universe. There are all kinds of military equipment to use, all have their strength and weakness balanced quite nicely.
Have you read any BT books? It stated there quite unambiguously, that mechs, while being powerful weapon platforms, never should be deployed in combat alone, without anti-BA and anti-air support. Mechs are not a wunderwaffe even by in-universe terms. But, alas, having too much mech-centred games in our past (don't get me wrong, I can't overstate how much I love MW series) and too much clan honour in our souls

we are used to think of mechs as the one and only possible combat unit. But it's absolutely not so. I'm sure, devs'll introduce a mech-only arenas in the final release for trueborn to conclude their duels with all the honour and respect to each other without any dishonorable interference. You just have to wait a little bit longer. But it's not the only way of fighting a war. The only one honorable way, may be, but not the only one at all.
By the way, none of games I played on public MWLL servers has the problem of some specific unit dominating all others. With too much aerospace of VTOLs there always someone on your side, who decide to became a dedicated AA and keep them at bay. If an enemy team is all-mech there's always a shiva coming in for an attack run. And so on.
So, Virt, if the only problem you have is with flyboys, don't mind it. Just concentrate on what you're good at -- piloting a big mean mech. I'm sure your team'll make an effort to support it's Atlas with some AA cover. But if you're not really good at mech either... Well, that's another problem.