I could sorta of see how someone could think Cassie is a self-insert/Mary Sue but the fact that this thread can come up with bad qualities of Cassie proves that she isn't. Despite her saintly qualities, she is called out a lot on her moralizing and hypocrisy by the other characters. And while her "betrayal" at the end of the series ended up saving humanity, it also got Tom and Rachel killed and started a new war with a new enemy with morphing technology so she doesn't get away with it. I think she was a much needed voice to the group and the series to complete deconstruct the whole "kid superhero" genre by giving a perspective not usually heard in that type of media. It's usually all "kick butt and take names."
Maybe since Cassie was an unpopular character, Reynolds and Applegate took great care to establish that Cassie IS an integral part of the group and drive home the message of the series about the right and wrongs of war and not the who beat who. I don't really see it as favoritism, I actually thought Rachel and Tobias (the few books he has had) got to do cooler plots but YMMV.
Actually, considering several people here have noted a shift in their preference of Cassie to other characters, I doubt Cassie being disliked would have been a reason for giving her all those superpowers during the series being created.
After all, the "bad qualities of Cassie" tends to be that even her worst mistakes ended up being superhuman insights that the others were just too stupid to understand at the time, or something. Not that I consider Cassie to be a Mary-Sue, but she's not moving back to the top of my Animorph list anytime soon.
Also, FWIW, it seems pretty certain they would have not won the war without the Yeerks getting the morphing cube - it's what caused the Taxxons and many other Yeerks to defect, making the final battle possible (the chance of the Animorphs getting another shot before the Andalites turned the planet to charcoal wasn't very good). And in that final battle, it was Erek King who disabled the Pool Ship's weaponry which allowed the Blade Ship to get away (though it probably would have anyway - they very heavily noted its lack of agility). Rachel was pretty much doomed any way that last mission ended unless the ship could have been disabled, and that was anything but Cassie's fault.
The Andalites weren't going to let the Yeerks get away regardless of the morphing cube - they create thousands of grubs every time they reproduce; it doesn't exactly take them long to build an army the instant they find a planet with suitable hosts. And I doubt
The One really cared in the least about the morphing cube.
All in all, I'm not sure how any of that could be pointed toward Cassie with any ease, unless we were going to assume Earth could be saved without being turned to charcoal without the morphing cube being forfeited.
As for plots, I'm having a hard time seeing how Rachel's plots could be considered cool compared to Cassie's :/ She basically never graces my favorite Animorphs books lists precisely because of the plot. Whereas Cassie's often do, even if I may be a disappointed with execution at times. But, as you said, to each their own and mileage may vary, etc., etc.