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Yoshi vs Samus I quite dislike because the matchup exemplifies all of Sakurai's bias in design. It's can be an extremely frustrating venture against a good Yoshi because you'll see things that intuitively you feel are just "wrong". It's a showcase of how bad and bias a designer he is. There's no other way to put it in polite conversation.
You can't trade, just forget about it. All of Yoshi's attacks have priority, he has big generous hitboxes that all connect and link well together and shield him from exposing his hurtbox. If they just hit buttons and you just hit buttons, they're going to win. Don't just hit buttons and spit hitboxes, you will get murdered.
His f-smash and up-smash have invincibility frames. Never forget this.
Yoshi's grab is actually just fast enough to grab Samus out of many of her moves. His dash grab, unlike his standing grab, is quite fast, as opposed to Samus' which gets worse.
Things that you think should work but just simply don't because Sakuria's a sob:
up-B vs. Yoshi bomb. Your "high priority" move - forget about it. You only chase Yoshi in low orbit, once he starts really flying high, you're not going to win short of a miracle landing our tiny invincibility frames at absurdly tight timings. Same for aerials. Stay grounded, charge your shot.
Yoshi f-air is a massive disjoint, like crazy huge you can't challenge it offstage at all. It almost always spikes as opposed to sourpot, it's pretty much everything we would want in our d-air. Because of this you're only ever going to recover very very low. Don't spit a missile and pray our useless projectile will do something, There's literally no point in trying to recover horizontally, high. You're going to repeat this cycle over rand over again because this is what Sakurai prescribed as your only option. And his b-air can still stage spike you recovering low so you need bomb mixup.
Unfortunately the converse is not true, Yoshi can freely recover to the stage whenever he wants because of his super-armor jump. He's almost impossible to gimp, and you should only try for a spike if he is only just barely going to make it back to stage. Even then an egg during recovery, which nicely covers his hurbox, may ruin your attempt, most likely. He basically gets back to the stage for free. You're going to charge your shot #1, then drop bombs at the ledge and charge shot him when he tries to land on-stage.
His command grab means sitting in shield is a recipe for disaster, so you can't reliably punish with up-B out of shield, also his landing lag is so low that in many cases you'll find up-B clanking with a stupid 3 frame jab that always perfectly links and has setups out of it.
From what I can tell, every one of Yoshi's multi-hits link on Samus flawlessly, and I honestly don't know or understand why or what has been programmed in the game that allows me to never escape them. The Yoshi b-air, is pretty much what we would want for our own multihits, long-lasting, huge hitbox, nice disjoint, and at any angle of approach or target vector everything connects, all of the time. The d-air, same sort of property, no matter what I try, whether I'm in the air, on the ground, at the edge of the attack, it just "works". I would really like to sit down with Sakurai one day and ask him how he could with a straight face say "I have no favourites" and then compare the multi-hit properties of Samus' arsenal vs Yoshi's.
Angle your f-smash, f-tilt down, always. Yoshi has tons of frames where he crouches and his hurtbox becomes very flat, just take my word for it and do it and avoid raging like a lunatic when it misses for no good goddamn reason.
Is this one of our worst matchups? It could be, at times it certainly seems that way. Your only, only saving grace is land-based moves out-range Yoshi's and he has no hard-coded straight up counter to CS. You're going to throw out a lot of spot-dodge, and a lot of SH-AD. That's just the way it's going to be until we get a real patch.