1) As an alicorn, she’s long-lived enough that she’ll be the one out of the Mane 6 still around for him to mess with. Could also be some twisted form of respect for her, maybe because he thinks that ultimately, even with his love for Fluttershy, the ReMane 5 are accessories to Twilight. He went for the ego boost idea because he dramatically misread Celestia using the Crystal Empire as a test to make sure Twilight was ready to be princess, so he cooked up something even more grandiose for princess 2.0.
2) He was lying to save his own skin and that was the best excuse he could come up with. Context was, he just got doublecrossed and made powerless, messed up big enough time the good guys might simply be done with him. Possibly for good, if Grogar’s Bell made him able to be killed. Whatever his actual plan with the Legion of Doom would have been in that case, he was definitely in a place where he’d lie to absolve himself of responsibility.
(I don’t believe this myself despite my dislike of him, but that was an interesting theory I read on TVTropes.)
3) It was the best excuse the writers could come up with after (supposedly, I don’t have links handy) changing their initial plans for season nine. I don’t remember the details, but something with Celestia, Luna and Discord needing to die to restore some balance or heal Harmony or some such, and the Legion of Doom was basically Discord balking at his ‘duty’ because he was (for the first time) afraid to die.