Samus's neutral game is dependent on stage control. Like you said, missile/ zair spam works well to achieve that control. One aspect that you need to get around is when your opponent starts to counter your missiles, whether it be from power shielding, shining, mario's cape, etc. When this happens, its your job as samus to punish your opponent. Thats her neutral game in a nutshell.
-Zair works great because it puts a hitbox on your opponent relative to when your missile hits. You'll either want to hit them on the startup of their reflect option, or after the missile is reflected so that zair eats the missile.
-Grab is amazing if you can move with samus. While its true samus is "slow and floaty", her wavedash and waveland are among the best. The idea here is to either grab your opponent before your missile hits. Most, if not all, reflect options cant hit samus within her grab range. If you can't get to your opponent before your missile, just hope they stay in their shield; that'll give you more than enough time to grab them with missile's shield stun.
-More missiles. If you're fast enough, your first missile will be reflected, but you're second missile will eat it. This is implying you missile cancel with a smash missile on the floor and a homing on a platform. Unless your opponent intends to stay in their shine, spam cape, or possesses godlike power shielding, missiles will overwhelm whatever option they decide to take. Again, you literally have to be frame perfect for this to be effective, plus your opponent needs to be close enough where they cant simply jump out of the way.
-Super Wavedash. Its easier to do in PM. Why doesnt any other samus utilize it? No idea. Missile cancel, swd, punish your opponent for basically anything they do in reaction. Whether you swd with a hitbox coming at them (Dsmash works great because of how long it lasts, and how it goes around samus), or you swd, cancel the momentum once you're behind them (Run the opposite direction) and do whatever your heart desires. Its fine if you don't prefer to SWD, but the idea here is to basically get to your opponent before the missile, like with the second option I described.
-Intercept their aerial evasion tactics. As fancy as that sounds, all you have to do its nair, fair, or bair them when they jump out of a missile's line of fire. Nair is good, but you want to time it correctly because it only hits in front and a little on top/ below samus. Fair is a really good sequence of hitboxes. The last one pops them up for major follow ups and combo potential. Also, ice fair and ice usmash are anti-airs as well.
Thats just the tip of the iceberg, implying that you are a safe distance away and are able to missile cancel without punishment. If you're not able to, that means you've lost stage control. It means you're on the defensive rather than the offense. Luckily for you, Samus is pretty much ALWAYS in defense mode. Most of the people you'll play against will want to always be next to you. Close range combat basically. To counter this:
-CC. Crouch cancel everything. Just spam Dsmash. Seriously, sooooo good
-UpB out of shield. If you're below a "battlefield top platform", land on it and follow up (preferably by ledge cancelling it). If not, either fastfall back down before your opponent, or find a ledge to cancel on. Most people arent fast enough to break your shield, and if you keep buffering it, samus will in theory do it in the first frame she doesnt have shield stun, AKA, instant punish.
--> Nair out of shield works almost just as well. Get frame perfect with it and you'll punish anyone who doesnt shine after a SHFFL
-Wave dash back. As simple as it sounds, its super effective. Bait out your opponent, and hit him with basically anything. Grab, jab, dtilt at low percents. Fsmash and dsmash at higher percents.
-->Wave dash back into ftilt is awesome. Ftilt in general is awesome. You can literally walk towards someone ftilting, and they wont know what to do. Get good at aiming it and you can hit people out of their aerial approaches.
-Jab cancel their shield. Know how to do this. If you happen to be next to someone shielding, grabbing may not be the best option depending on the matchup. Jab canceling is a huge mindgame with samus and if you're good at it will yield crazy results. Jab is one of her faster hitboxes, and surprisingly her second jab has good knockback in higher percents to setup an edgeguard.
-Don't shield grab. While it may work in some instances, her grab is downright bad. OoS might be even worse if you miss. Contrary to what I just said, shield grabs have a lot of reward, and it'll work on some moves that have a lot of ending lag. Your opponents will catch on QUICK as soon as you pull some off though. It's almost embarrassing if you get shield grabbed by samus. You have quicker OoS options to utilize, dont get stuck into thinking you can punish your opponent by shield grabbing him.
-Crawl. Super OP. Its like your jigglypuff, crouching, moving. Crawl titls can lead into Usmash. Crawl tilts in general can help you travel and is an awesome cross-up. Bait out opponents and dtilt/dmash them.
There is so much more I can type out, but I'm hoping this can give you enough ideas to work with. The idea behind samus's stage control is that you have a missile(s) out they have to worry about, and a moving samus they have to worry about as well. I mean, thats how I envision it. All the stuff I listed out are basic guidelines I usually follow in every matchup
, but im not 100% sure myself, feels larger than 3 frames though