Yeah, but one has better ways to deal with the opponent.
Mewtwo can probably do what Ness can and vice versa, but at the start of the match they are both ignorant about what the other can do and what they themselves can do with their abilities at their full extent, and that's where Ness gets his advantage.
He will catch Mewtwo off-guard sometimes because of his ignorance of Ness specific ways of using his powers. He will learn how to use the PK flash though...if he survives the first barrage.
You're missing the point, either can do that instantly via understanding how physics works and selective manipulation.
And both can dynamically detect how their opponent is using their psi and oppose and counter.
Their movepools isn't their starting abilities, it's a tiny portion of what they know how to do with their psi, a very very tiny portion.
The control they've shown combined with their raw power means that either will be able to use a move equivilent or far more powerful then PK flash from the onset,
Creating micro-black holes in vital organs, cutting vital arties, disassociating molecules, for both characters that's in their grasp from the onset.
Both characters have access to incredibly creative ways to surprise their opponent using psi in equal measure. Victory will be determined by who gets in first, which because they have equal ability to surprise and defeat each other will be 50-50.
So no, they are not limited by their techniques, they are true equals in every sense of the word with nothing to establish otherwise.