Alexis was meant to be mandatory - the plan was to be able to battle her after the witches (or before, which makes the witches bosses skipped), before being able to battle Aidan.
The Azehr bugs strike again :-/
I'll see if I can fix them; one Azehr bug is out of my control though (namely, beating him while he grabbed Serenity - this appears to be possible in the original Cave Story too).
Moving blocks will have to deal 200 damage, then.