There's no real way to fix Ripley's arc. They finished it beautiful, warts and wall, with Alien 3, and then they decided to reopen it again.
As to the Ripley/Alien hybred thing, they could have maybe done something interesting with that in a sequel to Resurrection. Ripley gave the queen a human reproductive system, so what could the queen given Ripley? What might have manifest in days, weeks, months or years after she returned home? I'm just saying.
As to going into the future, again, that future was at least somewhat written out for us in Resurrection. You'd have to go in further ahead of Resurrection, 4 or 5 hundred years from now. Hey, we'd be in time for that Firefly/Alien crossover! Haha!