I don't like organizing my thoughts unless I get graded on it or paid for it. So random stream of consciousness go:
Ban FD. Jiggs has full aerial control there, and you can really only move on the ground. If she gets that extra axis of movement to work with and you don't, the matchup goes from bad to terrible.
Ok, now you're on a stage besides FD (hopefully Yoshi's, Fountain, or BF). Now you need to learn to move around the stage as fast and as far and as accurately as possible. I do this regardless of matchup because that's how I like to play, but in this case I just don't see how you can win otherwise. You need to be able to be able to waveland off a platform, fastfall under Jiggs as she tries to fair you, and double jump uair from below. You need to be able to full jump uair, and waveland across a platform to catch up and fsmash before the pressure game resets back to neutral (because neutral = in jiggs favor). You need to be able to waveland off a top platform, off the side platform, back onto the top platform, and fall of with a fastfalled bair as Jiggs floats towards you. How situational are any of these? Extremely, but you need to be able to know and consistently do anything Samus can physically do on all the neutrals, so when you see an opening or the potential for an opening you can get there and insert your hitboxes wherever you think Jiggs is going. When the puffball constantly has the option to hover around basically anywhere and place her stupidly quick, stupidly positionable, stupidly powerful aerials all over the place, you NEED to be able to see and realize gaps without even really thinking about it.
Talking about Jiggs fair or bair or nair and how to "beat it" is worthless because those aren't just one move each. Retreating and falling fairs that don't hit the ground (allowing for the possibility of a double jump), full jump fairs when moving forward, shorthop fairs that move forward and then back slightly, rising retreating fairs that give Jiggs the option to land on a platform, those are all completely different attacks with vastly different options for you. Make sure you aren't seeing a fair and thinking "Oh yeah I know how to deal with that" and then not learning when you find that it's different and your strategy needs to be different as well.
Missiles are not for hitting Jiggs. Missiles are for forcing her to move higher, shield, or throw out an aerial, all of which will hopefully give you an opening or a positioning advantage. Let's look at those options and what you can do about them:
Shield: You can grab -> dthrow -> charge shot or nair. You can also run up and wait/shield to see if you can figure out any kind of pattern for when you force the opponent to shield. Like, do they know the missile doesn't have enough shield stun to lock them in for the grab, and buffer a roll or spot dodge to avoid it? If so, what way do they roll? Remember it, and try to take advantage of it later when you need that kill (shoot a missile, run up the shield, WD to where they'll probably roll and dsmash, for example)
Midair jump over the missile: Anytime Jiggs is higher than full hop height (but low enough to hit), you should attempt to get under her and uair through her soft pink underbelly. In my experience, that and wd back utilt are the main ways to get hits in.
Aerial through the missile: This is the main strat I see from good Jiggs, because it's really easy to destroy missiles with her brokeass hitboxes, and they can hit you to if you're following the missile too closely. Usually they'll use fair or bair (sometimes nair). When they do this, congrats, you've forced Jiggs to do an aerial in a place where you weren't. Now you have to figure out what to do to punish that (very small) lag. If he used a rising aerial, you can try to get underneath and catch him with the top part of the utilt, jump up and fair, or jump from below and uair. If it's KO percent time, you can even try for a nair. If he falls through the missile with an aerial, and you know where he's going to land, they you're free to place any long Samus hitbox at his landing spot at your discretion. KO percent? Try an f or dsmash. Low percent and you need to do some damage? Utilt should lock him in place on the ground, so you can dtilt to uair whatever you usually do when an utilt locks an opponent in place. Mid percent utilt is probably the best choice too, because it should bounce him up low enough for you to get a nair or something in.
Actually in general utilt is so good in this matchup. There's like no lag after it, Samus' legs are crazy long, it hits so far above you, it's just great overall. Try wding under a full jumping Jiggs and turn around utilt, find the spots where it works, it's kinda hard to describe when unless you've seen it.
On recovering... Jiggs will go out there and smack you. So you need to have full control over your recovery options. Full DI on bomb jumps (mix up which way you hover around too); save your double jump as long as possible, sometimes you can use it to go under the Jiggs and aerial her from below, buying you some time; airdodge through attacks and grapple when you can; make sure you DI straight up if they manage to hit you so you'll have more vertical room to try again (and also so you'll live); if he stays on the stage, recover low to wall jump -> turn around missle is a personal favorite of mine, it can get edgeguarders away from the edge long enough for you to grab the ledge; upB from below through Jiggs can knock him away, use that sometimes. Generally though, never recover the same way twice, Jiggs has way more control out there than you, so you need to be able to adapt on the fly with as many options as possible. Also as a general rule never go for a dair or a nair or a fair while you're out there. It's just not worth it, it's not safe, Jiggs with good spacing will just hit you.
When you have a shielding Jiggs up close... Don't smash attack. Don't dash attack. Don't downtilt. SPACE PERFECTLY your ftilts and utilts and jabs (and jab cancels). One thing that I've had work is (spaced!) jab on the shield to wavedash back fsmash, but that was on a "jump out of shield ASAP" happy Jiggs player. Learn what this specific Jiggs does to get away from shield pressure and try to predict and abuse that.
All of that is weird, oddly specific snippits of info that may or may not help you. Sorry if it doesn't, and correct me if you see something blatantly wrong.
