*Alia’s hints are permanently disabled
Were any of them important?
Unless you like being instructed on the most basic of gameplay (and this happens quite often, in every stage), no they did not have anything useful to offer. The only time you could argue they would be useful is the training stage (but do you really need to be told "press up to climb a ladder?")
In the future, I plan to implement MMX6's way of handling Alia's hints: an icon pops up in the corner and a sound effect plays. You can press select if you want to read it or simply ignore it. I also plan to make all the cutscenes able to be skipped by pressing start (again like MMX6).
*Keep both character bonuses regardless of which is chosen
Why is that good?
At the start of the game you get to choose between X or Zero. X starts with the Force armor and Zero starts with his Z-buster. Whichever character you choose, the other loses their bonus. Since the the Z-buster is pretty useless, there's no reason to choose Zero for the intro stage, and having the Force armor is much more beneficial (you can choose between the characters at the start of every stage). By keeping both character bonus regardless of which is chosen, it gives the player some incentive to choose Zero at the start.