I think there's also the timeframe that play a big role.
Between Xcom Enemy Unknown and its modern remake there are nearly 18 years , meaning that the people that played and loved to death the original Xcom weren't going to be the majority of people going to play the modern remake, there's a whole new generation of people that were born in between and were by then in age to be interested by this kind of videogame and it was well advertised enough to attract even people having never heard about the franchise.
So there's a big percentage of people that very likely never played the original Xcom, making this modern remake gameplay and system changes to face a lot less "fan resistance".
And with the remake being in a genre that is not usually seeing such big production value, it probably had an easier time than a game like Xenonaut that was another recent Xcom clone.
The difference in timespan seems important, but another difference between the rejection of Call to Power and the acceptance of the new X-COM has to do with the presence of the original creators.
In CtP's case, Sid Meier was still a very public figure and making 4X games at Firaxis. When CtP came out, it would have been rejected for almost any slight deviation simply because it was not a Sid Meier production.
In X-COM's case, the original creators had moved onto to other things. Does anyone even know who they are, without googling? Unlike Civ, most X-COM fans have no idea who the creator is so it's easier to transfer the legacy, especially to an established 4X icon like Meier's Firaxis.
Even MOO fans know who Barcia and Emrich are because they were involved in all 3 games. But the Gollop brothers?