Well looking at the grid of the new maps, it looks like the amount of gates has dramatically lowered, it looks like one per area, making it three per region (Only looking at the maps, can't say for sure.). If this is the case, while I can't say if Anima is staying or going, but I am very sure it is going to get some form of adjustment when 2.0 arrives.

My opinion on Anima, I can't really say until I see how the new maps are. Currently, I try to not use it as much as possible, only use it when I want to get to Turning Leaf or if an event is starting and I need to get there quick. If I am on my own time or farming, I will take the extra 5-10 minutes to travel there. So I wouldn't be sad if Anima left, but I am fine with it either way.