I think what it comes down to is that you can't please all of the people all the time. I'm not completely happy with this series either, but I'm not going to #$#@# about it based on my opinions of who should win or who should or shouldn't die. The animation in this is really well done. We got to see some of our favorite characters again, and they made it more enjoyable for the older crowd.
As far as the writing goes, this isn't Citizen Kane here. We're still talking about a 60 minute cartoon. If you think you could write a better script, kudos, but I don't want to hear about it. And because it IS so short, they don't really have a lot of time to flesh out the conflict between SS and SE, so they packed in the action and let the good guy win. Big deal. Hasbro is not going to kill off the Storm Shadow character completely, otherwise there would be no more SS toys and therefore no SS money for Hasbro.
I like it and thats my two cents.