I just finished, and have some comments in no weighted order?
Logically 3 ships will not affect significantly what is transpiring in the Alpha and Beta quadrants, and might be more useful where they are.
I may be in the vast minority, but having a lover or partner where one is superior to the other in the chain of command is a bad idea.
I wonder if this story will be used as in the comics industry to reset or change certain historical details that could not ordinarily be done easily.