Samus does not necessarily recover or edgeguard better because needles really shut down all of Samus' recovery options unless you go very high. The bottom line in this MU of course is to not be grabbed. Like most MUs, try to zone them out with tilts, etc. Don't rely on missiles too much unless you are good at varying their heights so that they go above grounded needles. Good Sheiks will run up and shove their shields in your face, hoping you will do some kind of panic move, be it tilt, spot-dodge, or upB. Don't fall for it. If the Sheik dthrows you, unless you know that they don't know the timing of the f/uair punish, DO NOT try to DJ out. All you will accomplish is the very beginning of the DJ (and you and your opponent will hear the sound) and then you'll be offstage or high in the air with no DJ, which is always very bad for Samus. I believe you can start jumping out once you reach very high %'s (I think 140%, but don't quote me on that) because Sheik can't reach Samus in time. CC is obviously good, but good Sheiks and even not-so-good ones are all aware of that. If they're displaying a tendency to tilt and DA too much, then CC dsmash away.
If you manage to spot-dodge a grab, you can generally punish with a fast dsmash. Spot-dodges are bad for every char if they're predicted, but I wouldn't necessarily say they are terrible for Samus simply because Samus' spot-dodge is so good.
If the Sheik is very jumpy, you can react to the jumps with aggressive fair combos or you can try to keep her out with utilt. DO NOT try to DJ chase her if she DJs away from you. Sheik ascends and falls too fast and Samus is too slow, so you'll be baited and punished. Oftentimes, it's better to just wait on the ground and attempt to catch her landing. Dtilt and dsmash are both good options for this because they have a lot of range and set Sheik up for even more punishment. Dtilt is especially good at catching landings because of its deceptive range (I think that move actually has more range than dsmash). However, be very wary of needle set-ups. Charged needles can guarantee you'll be grabbed, even if you shield them, so don't let yourself be caught in those triangular positions, especially in front of a platform.
So bad Sheiks will DA or jump fair at you way too much. However, many good Sheiks will dash in and pop their shields up. If your move was laggy enough, they'll WD OoS in for the grab. If not, they won't force anything and will attempt to catch you slipping later. The reason this MU is so terrible is that we really have no good way of stopping this. If we space our moves, we can avoid punishment, but our best options (tilts and smashes) are so negative on block that Sheik doesn't really care too much if we hit her shield. Obviously, the solution is to grab, but we all know how awful our grab is. Nevertheless, we need to go for the read and grab. It's kinda scary because really good Sheiks with fast reaction times can straight-up react to Samus' grab and roll around/jump over it. One way to kinda circumvent this is to read when the Sheik will put up her shield and grab ahead of time. Both grabs come out on the same frame, but dash grab has less lag (still super-punishable, though) at the expense of range while standing/JC grab can catch rolls back but is a guaranteed rest punish. It is SUPER important to know your follow-ups off of grab because Samus has some of the more awkward grab combos. Off of dthrow, with DI in/no DI, we get fsmash, and with DI away, we get DA (which can lead to more DAs or nair, depending on subsequent DI). We may get more things, but that is the general flowchart I follow. There are a couple other decent options to deal with shields and Sheik in general, though:
- Bombs. Bomb wavelands, bomb dair, etc. Bombs really eat up shields. I don't like them that much except on plats, though, because it usually involves me going into grab range.
- Wavedash behind Sheik's shield. This is probably the single best position you could ever be in against Sheik. She can't grab you and her bair OoS will probably go over your head. Meanwhile, you can pressure her with CC jabs to prevent jumps and WDs OoS and get ready to catch the spot-dodge or roll. This is probably your most optimal choice, but it won't be easy to just cross through Sheik like that. Doing so under cover of a missile can help.
- Missiles. Missiles are decent because they force some sort of reaction out of Sheik, and that reaction tends to give away how she habitually deals with missiles in certain situations. Remember, Samus is a conditioning character, meaning that it's very important that you observe what your opponent tends to do in specific situations so you can promptly punish him. At the same time, you have to make your opponent respect certain options and then use that mindset to 'disrespect' him, so to speak, by hitting him with counter options. If you run immediately behind the missile, you get a free grab or dair approach (dair is pretty positive on block) if Sheik decides to shield it, but you have to be wary of the possibility that she will roll or spot-dodge (although grab and dair both tend to catch spot-dodges); dsmash tends to catch rolls behind Samus pretty well. Alternatively, you can just continue to run/WD past Sheik as the missile hits her shield so that you are now in the prime position behind her. Against bad Sheiks, I like to run past > fsmash because they immediately drop their shield the moment you cross them up. If Sheik decides to clank on the ground with the missile, you can actually punish the clank lag with anything that's fast enough. Samus can DA through PS'd missiles, so keep that in mind. If the Sheik is very jumpy, she will probably try to jump over a large portion of the missiles, so act accordingly and punish. The one counter that kinda messes up the missile option, however, is needles. Sheik can simply launch them on reaction to you landing, so it's a good idea to learn how to vary your missiles' heights so that they go above the needles to hit her head.
- Charged Shot. I'm pretty sure a fully charged shot is plus on block. Of course, it's a lot more satisfying to actually hit Sheik with the shot, but the fact that Samus can move first for free after hitting Sheik's shield with it can be pretty useful. After shielding an unexpected Charged Shot (which will catch spot-dodges and rolls back, mind you), opponents often try to drop or exit their shield because they are afraid of an imminent shield-break or poke. If you are close enough, you can easily stuff this.
If you're caught in the air above Sheik, mixing up your descent with the regular bombs and fat FF nair can stuff many of Sheik's attempts to hit you but don't hang around there too long because she can easily aerial through the bombs. If you're stuck on a platform, you might want to wait a little bit (while making certain to either light shield or angle your shield down) because many Sheiks will eventually try to jump up and hit you, which you can punish or just escape afterwards. Still, being above Sheik is probably worse than being above any other character in Smash, even Fox or Marth.