Really, i dont consider any projectile game to determine a matchup.
"At the highest level" dodging and evading projectiles isn't a character specific dilemma, its a mental and almost universal to all characters. The characters that have projectile reflecting moves (Fox, Falco, Doc, Mario, Zelda, Ness, Mewtwo*) don't rely on them to beat projectiles. They may mix them in occasionally, but overall its game mechanics (jumping, shielding, powershielding, ect) that are used.
Projectiles are not very good in melee as compared to other fighting games. Some do a good amount of damage and others have speed, but none are both fast and strong**. The ones that are slow, you evade. The ones that are strong you block. When you talk about mewtwo's uncharged shadow ball, it is neither strong nor fast. I double anyone is seriously concerned about getting hit. They won't sit and take them the whole game, but if they try to jump over one and mess up, nothing bad will happen besides taking the 3% or whatever it does.
When talking about a matchup, especially one like zelda vs mewtwo, you must consider a few things.
1) spacing tools. Who has the most range in close combat?
2) punishment from a mistake. How effectively does each combo, and on average how much damage does each combo do?
3) KO potential. What moves does each character have to kill with? Do they have lead in methods from traps or combos?
Now, for this matchup, this is how i analyze this:
1) Zelda has more range. Her dash attack, fair/bair, and fsmash are all longer ranged with more priority than mewtwo's moves (afaik his best ranged move is his bair, his fair has abysmal range, and his nair has priority but no range)
2) Mewtwo's best punishment is probably dtilt to ftilt or dthrow to dtilt. zelda's kicks are sort of like ganon's hits, they are complete punishment by themselves. Overall, i call it about even.
3) Mewtwo can kill with bthrow, uthrow, and fair. All of them require zelda to be above 120% due to her weight. To set them up, he must be very close range. Zelda's spacing tools are KO moves. Mewtwo is light and dies fairly early to them (80%-100% depending on stage location and DI).
Now, from what i'm seeing, zelda simply needs to stay close but keep mewtwo out of her zone. Mewtwo has almost no approach on zelda, and no real method of killing her without her making a mistake and letting mewtwo get in close on her.
*Mewtwo's reflecting move doesn't change the owner of the projectile
**Mewtwo and Samus' fully charged neutral b moves are both strong and fairly fast, but require a full second to charge.