My squad had just dealt with Highpool, and when Kate briefed me on the matters I realized that a desert with lots of oasis probably needs less mutant plants more than a small dam. The radio transmission says that Highpool is expecting Skorpion backup, do they actually appear in Highpool if I choose Ag Center instead?
Since you cannot save both Highpool and Ag Center at least one of them will be destroyed. Which one you save is up to you and is supposed to be a tough moral choice, but also about which additional character you'd like to have (Rose in Ag Center, Vulture's Cry in Highpool or none).
You can, however, let both get destroyed. I'm not sure about the conditions, whether you simply have to wait a long time (in my experience, time passing rarely has any influence on the quests) or whether you have to visit both places and then leave.
You can only save one of them, I personally saved highpool as I preferred the npc you get there.
As someone mentioned in the comments, you can find the scorpions in highpool and the reason why they didn't respond in the same location.
From what I have heard if you take too long in going to either location then they will both fall, but I think that takes a fair while.