pod activations system is only slightly changed
The yellow alert system and the new sound mechanic fundamentally changes combat for the better. It used to be in EU/EW and X2 that you would hesitate to advance to take flanks, because you would activate another pod, and it became really gamey with you scouting ahead to make sure you didn't activate anything while launching rockets and grenades all over the place and nobody knows shit. Now even if you try to avoid them, they will come in on yellow alert because of gunfire and if you're playing on higher difficulties, they will often take offensive actions too. So you might as well bite the bullet and activate on your own terms.
It's not perfect, but its a lot more simulationist than before: pods don't all converge because different pods have different jobs, like guarding the objective and whatnot. If they did communicate and all converge on your squad, you could easily send a shinobi to deal with the objective while the rest of the team plays decoy. Some pods converge in a highly tactical way, like flanking you with a second pod. This isn't always executed right but I think their approach to pod behavior is good.