Oh no you didn't!
At first, I was thinking that it was the final battle, but with the transporter getting destroyed, now you've caught my interest. That's a good thing I like about this is the fact that the plot does loop you in a bit, although I do think Shadow being brainwashed was a little rushed. Would have enjoyed seeing that more. I do like the new cut scenes and the intro, giving it more of an RPG/Sprite movie feel and thank you, THANK YOU for the cut scene choice.
Although everything is borrowed from other sources, I do think you've programmed this well. Even though there is no leveling system, there is some growth shown through the increase in HP, power, and healing. The new addition of the Giga can also be considered an increase in growth, probably because now that everyone is together. I find the increasements for this new power fair and it is definitely good for those that want to take off some of the challenge to fighting eg. Bowser.
The fighting system works well and I like the edition of naming the enemy attacks.
If lacking anything, it's probably in the fact that there is no original content outside of the plot and fighting system of sorts. Overall though, it's a good game and I do hope to see more from the series and see it develop more and more. It definitely shows growth from the first one. Good luck and can't wait for MMS RPG 4.