It's not so much that there are differences that are the problem, it's the socially designated roles that are the problem.
Men and women are different. That's just a fundamental part of biology, and there are certainly some mental aspects that are fundamentally different as well (such as brain usage). And, in fact, gender identity tends to be one of the first things that kids really latch onto about what makes them them. Which is fine, by itself.
However, those differences should be allowed to manifest themselves naturally. If boys tend to prefer trucks over dolls for whatever reason, that should simple be accepted. A boy who prefers to play with dolls or a girl who prefers to play with trucks should also be accepted.
The problem, really, is that such things are not accepted. The 'normal' set of toys is not only expected it is often enforced by adults. Like people said earlier, it's more often the fault of adults that kids who act outside the norm are ridiculed.
The real trick, I think, is not so much to strive for actual equality but to drive for equal acceptance. It doesn't matter if 90% of boys would play with trucks over dolls or if 90% of girls would rather play house than shoot nerf guns. We should accept what people choose to do for themselves.
Same goes for everything else, too. Most women may not want to be construction workers, but that's no reason to penalize the ones that do. And until we can get society past that mental block of 'but..but...women do X and men do Y and...and...we hate stuff that's different' equality is going to be a tough fight.