If he had the most data, but was not included in the game then that was an intentional decision. Time restraints means a decision has to be made and that decision was intentional.
Then let me rephrase that, there's no reason to believe that he was cut with the intention of always being a scrapable character. Time constraints may've just forced his hand.
I do not think it is coincidental, but only Sakurai really knows for sure. Perhaps, Mewtwo's Shadow Ball would have different stats.
Considering that moves of the same (or similar) properties like Bowser's Fire Breath and Charizard's Flamethrower are present, yes it can be coincidental.
Both moves act the same with the instant death charge. But saying the move was taken from Roy is speculative. Ike did have his B move replaced. This we know. And if Roy's data file was around there is definitely motivation to take his move.
It's completely conjecture to assume that what you're saying was the case, there is no proof on the matter that Ike's move is derived from Roy's. Besides, Sakurai gave his reason for the replacement as he felt it was broken, that's it, there's nothing else to it that he added and thus basing a theory off of that is completely unsupported.
Just because one move is similar doesn't mean that said character was meant to be their replacement.
Priority was given to Lucario. So you can argue that Lucario was not cut for Mewtwo. I still disagree. But what is a fact is that Lucario had priority over Mewtwo (a veteran, non-clone character) to be added in the roster.
Yeah, so did PT and Jigglypuff, Lucario is not a special snowflake, they're in the exact same boat as him. All three were prioritized over Mewtwo, but that doesn't mean any of them were intended to be his replacements.