X and Y chromosomes don't "want" anything-they are not conscious. I know that sounds obnoxious, but it's very important in evolutionary biology to understand that there is no agency and no intended final product for natural selection. I think the best way to think about it is like this: let's say there's a mutation on the X chromosome that happens to make females more fit at the expense of making males less fit. It seems possible that the evolutionary arms race that this establishes (i.e., males bearing a mutation that compensates or overcompensates for the new expense of the mutation that, say, their successful mom gave them, would then start to sweep to fixation in the population, and so on and so on) could result in population collapse. Apparently, there's theory out there that confirms this: http://www.els.net/WileyCDA/ElsArticle/refId-a0003669.html. Also, I vaguely remember a paper about toxic sperm (vs. female mating behavior) in Drosophila melanogaster suggesting that populations could collapse. As Bonduriansky mentions in the link, though, one resolution to the arms race would be the evolution of genes that get expressed very differently between the sexes (i.e., a gene that is good for a female but terrible for a male would evolve to only be turned on when it's found in a female). I hope that helps?