I'm definetly for new anomalies popping up during the game. Especially when you're trying to avoid war, there's no turnaround when you miss out in the early game. I would even go so far and have no or very few anomalies exist at the start of the game, so the new ones appearing are the major part of it. The de luxe version would be if both rates (initial / appear) were adjustable, of course
There should be a notice in the news that a new anomaly has formed, by the way. The AI won't miss it, but a player will usually not notice a new spot on the map, so he's at a disadvantage.