She was going through the motions most part of the time in 3rd and 4th films and somehow managed to win (quite questionable victory in A^3 though), whereas in 1st and 2nd film she always stroke me as a strong personality. I would love to see that in her again :-)
Questionable victory in Alien 3? She killed the alien and stopped the company. Done.
A:R is about clones not the real deal, hence fleshy aliens with queen legs and a queen with a womb.
Ripley's personality is at her strongest in Alien 3. She has to deal with everything on her own right from the opening scene. The one person she connects to after she finds herself there is Clemens, who is killed as a reminder of the path she is on. She kicks a lot of butt in Alien 3 and held her own even when faced with a possible escape (aka Bishop's menacing promise of removing the embryo and helping her achieve a life she ought to of had).
Personally, I've actually never been satisfied with those endings because they don't effectively stop the human race from contacting the creatures again. See Prometheus.
Prometheus is set long before Alien 3. Not after.
But you're right in saying Ripley could potentially be destroying only a fraction of the aliens that might be out there. But her intentions are all the same.