That's not an issue with the aiming mechanic though. That's more of an issue of how character models interact with cover that runs contrary to how most modern tactical games use cover. If you think about it, PP's treatment of cover is closer to X-COM; the best way to not get shot is not to be seen. It is still nonetheless frustrating to see a triton sniper score a head shot against a trained soldier who should really have an animation to actually use high cover instead of just standing there.
There is an animation with low cover, at least; character models will crouch behind it, so ironically low cover actually is a little less annoying and probably more effective to use than high cover.
The aiming mechanic itself is fine and adds a fair bit of tactical flexibility to the game.
The reason it's related is because most games (including Xcom) determine cover using tiles, if your character is on the right tile, you're in cover, regardless of their animation. Because Phoenix Point decided to implement their "aim at enemies" mechanic, they had to instead use a system whereby cover is based purely on how visible you are. In a tileset based game, this is horrendous. Even in a "free movement" game like Warhammer 40k, this is horrendous.
So yes, this IS the aim mechanics fault. It has affected the rest of their game design, and it looks like it did so in a really bad way.