I do agree that the ending is a bit rushed. But that's honestly the expected result. It's been shown multiple times that Mewtwo is about equal to minor legendary pokemon like Articuno or Landorus. And usually multiple minor legendary pokemon are required to even come close to defeating a Major one like Groudon or Ho-oH. Heck to beat Zygarde it took Mega Mewtwo and 5 other Mega Pokemon. Regular Mewtwo is equal to deoxys based on the Fire Red arc though maybe a bit stronger since a regular Deoxys normally can't change instantly between any of it's 4 form. So Deoxys probably wouldn't even stand a chance against regular Rayquaza much less Mega Rayquaza using it's signature move. So nothing other than a one shot would make sense. And it's not like they have much of a direct control over Rayquaza they are just generally guiding it and providing it mega key stones. Rayquaza would have no real reason to care about Deoxys so I doubt it would go out of it's way to save it. Though I doubt this is the end of deoxys story. It's probably going to survive somehow and given previous events that wouldn't be wierd at all. It's probably going to come up in a future arc and get a proper ending. Though I do wish there was a more definitive ending.