I was comparing it to CM Arceus, not Geomancer. I know Geomancy and CM are different :/
Here's the thing about Power Herb Geomancy: it works ONCE. Once you use up Power Herb, its gone. If you have to switch Xerneas out or it gets phased out, next time you use Geomancy you have to charge it up, which is an obvious and extreme disadvantage. This limits Xerneas to lategame, when it is least likely to be phased out or its counters/checks are weakened and it can take full advantage of the SINGLE +2/+2/+2 BOOST it can now safely set up. CM Xerneas does not face this limitation can be used to set up at any point in the game. They are played entirely differently, so one is not better than the other. Comparing them would be like comparing LO DD Moxie Gyarados with Bulky DD Leftovers Gyarados; they do entirely different things. The reason why I said it would be the "Flagship" set is that it is just "safer", and past experience shows that skilled players will stick to safer and more reliable sets.