I think what will be fairer might depend on what sports they are; I think that they will have to be considered for each kind of sports, why they have sex/gender segregation, whether or not you should have a segregation at all (and if so, if it should be by something else instead), etc.
Sports that don't need segregation and where people don't want segregation don't usually have it.
There is no rule that says women can't play in the NFL for example. A combination of biological realities, a lack of interested women, and cultural expectations have just naturally resulted in a segregated system. Any woman who is qualified for and interested in playing in the NFL can and should.
It's fine for people to decide who they want to play with/against too even if that means by definition that some people will have to play somewhere else. If someone wants to start a league of dart players all named Bill so what? May the best Bill win! The thing about sports divisions that segregate themselves (by name, region, age, gender, etc) is that they also limit their success. The best dart player named Bill can't claim to be the best dart player in the state without playing against people with other names.
If people are happy with their accomplishments within whatever division they're comfortable playing in, we can be happy for them too.
