The scope of their goals was " Make a Mew, but stronger " in both the original group and this group's case. If that's their aim they'll probably be looking to enhance the same things with marginal difference. Since they're just enhancing Mew they produce Mewtwo.By that logic, if someone were to just genetically enhance Mew's Dragon type capabilities, out pops a humanoid purple Mew and not just a normal Mew with more powerful Dragon moves.
So I guess they'd produce a Mewtwo that naturally knows Dragon Pulse; a move it normally cannot learn, in your scenario.
Except, as I've told you, there is no indication that the scientists knew of the old one's existance.
They wouldn't need to.
They're not trying to make a Pokemon in Mewtwo's image. They're making a stronger Mew.
Show me scientific proof that all Japanese children are mindless sheep who are 100% incapable of noticing glaring continuity screwups.
You can probably just Google children and memory and pull up some reading material. The general consensus is that children as young as 2 could form memories about things they've seen and experienced, but their ability to recall those memories fade as they grow older. That extends to other aspects of their mental development. Their ability to understand a story, notice inconsistencies, and make their own decisions also improves with age.
That's why children's programs fall into a predictable routine. It may be silly to adults to have to explain how things in this particular universe works every episode, but children are more forgetful. We even see colors of that in Pokemon where Ash feels the need to dex Pokemon he clearly has seen and interacted with before. It's not for his in-universe benefit. It's for the benefit of the young audience who might not have seen a Koffing (a particularly infamous example) before.
Also "get over it". Elitist, much?
I'm more a realist.
A lot of people went into this with absurdly high expectations ... as if they haven't been watching this show for 14 years and we haven't been dissapointed by the current region at almost every turn.