They eliminated only the F4. There were still X-Men on the console version too. They just didn't include the entire PC roster overall at launch.
Sorry but I'm not gonna believe it's a coincidence that Marvel Future Fight didn't include her even when they were doing a Civil War tie-in and we got her replaced by Sharon on TeamCap, and then when they managed to get the X-Men rights, one or two patches later Wanda and Pietro are suddenly released too. Literally every game that didn't have X-Men also didn't have her.
Besides that, why the hell would Marvel make her most expensive and other Avengers cheap? If anything, the more popular characters should be more expensive, the other way around makes no sense.