High recovery is pretty bad in this MU yes [unless he can make it back via DJ and airdodge - then it's doable for sure, and a mixup I actually rather like, since if it looks bad, fastfall DJ and recover lower], but grapple lets Link go low (I'm not sure if you can morph ball bomb to somehow screw this up, but I think at worse he has to pull up early and get hit) and so does just falling below the ledge.
Link's got a few reasonably good options below the ledge against Samus. You can up+B for vertical sweetspot, which can often be used to avoid whatever (missiles for sure, I think maybe ftilt), and if I'm not mistaken, Samus can't utilt or dsmash him without getting poked if Link is facing forward (or spacing is very tight - and if Link is going for the horizontal sweetspot (i.e., max range horizontally), it's even harder). However, this is prime dair territory, morph ball shenanigans perhaps, and it can also be a nair from above or dair if you went offstage for it. @
Litt
is utilt/ftilt landable on Link when he's spacing up+b if Samus has good timing or not? I don't know, but I think if it is, it's very tough and a good Link can still mix it up to try to fade away to avoid utilt or into the stage to hit with it. [I don't have a person in my dorm who plays Samus or a person who likes testing things, or I'd go ask them to help me check something quick and get back with a solid answer - sorry.]
Link can also go slightly above the stage (like with his head, still grabs ledge), to better poke with his up+B - this is something I do a lot, as it makes it beat out ftilt (it seems to me - she gets hit) and utilt usually, and you have to have a low missile to catch this (which his up+B may do enough damage on the last hit to detonate safely??? I don't know, but that's the hit we need to break bombs open, so it's possible this could work too...). Still vulnerable to dair and probably eats a fully charged charge shot (bleh...).
Link can also up+B so that he lands onstage, but basically immediately after finishing up+B - loses to missile (and charge shot!) but I think basically always beats out ftilt and utilt [this is started while below the stage lip], and is basically impervious to dair (especially with good SDI) - a good mixup in my opinion, bad if it's the only option of course (since you get a free charge shot every time!).
Missiles to force him low and trying to dair him or space a tilt (I don't know how much this works, if at all... that's why I asked Barbie) would seem the best option usually, but if you whiff dair Link gets back for free (and if Link is good at meteor cancelling you actually will get hit for landing dair - kind of silly but it's the rules of the game), and if you misspaced a tilt Link clips you with his up+B and is back for free, so while Link's options aren't great or anything, I think they are good enough that Link can make it back even against a very proficient Samus... eh... at least half the time? I say this guessing that if she's perfect, since some of these basically have to be read or guessed, since Link's fastfall is so fast he can look ready to do early up+B but fastfall and like 5 frames later go for sweetspot up+B (or whatever it is), or tether and tether at a place where he almost grabs ledge, "refreshing" all his options except tether.
Incidentally, Barbie, can Link dtilt a sweetspot up+B from Samus??? I don't know, but if he can, that's extremely hilarious-looking edgeguarding, and if you miss the meteor cancel, you die, while if you cancel to early and he manages to space it to not get hit, that's a free up+B or fsmash back offstage. And if he whiffs it and hits the tip (no meteor), he can still go for a uair, nair (if low enough), or even dair (hardest one, probably only works on spacies but if you don't nair out because not expecting it, good luck...). This would also make Link's edgeguard options on Samus even better if he can hit her back out after using tether and has good spacing with it [something I didn't note because Link's dtilt is not an edgeguard I use frequently].
Dunno if FD skewed your understanding of things or not - it's not a great stage for Samus unless your brother plays a Link that doesn't use a lot of projectiles, at which point possibly? Projectiles are most important on FD of all the stages, with DL being second and PS being third (being good at them on PS makes it a good Link CP because of the low ceiling and moderate side blast zones favoring him, plus space to camp well - but most Samus mains don't CP this which is why it's third, not first). Now, that's not to say they aren't a vital facet of the MU for Link to win on all stages (they are in my opinion), but if he's aggressive on FD, he's giving up easily his biggest tool, and since he can't platform camp to avoid low missiles (i.e., use plats to avoid missiles while readying projectiles), missiles become better (though Link can still outpace missile production, but if he's not (because not many projectiles) and not good at clanking them, missiles go from being rather bad to really really good, since Link being a little slow means he has to work harder to approach without a tool to lock you down since he's also dodging explosive projectiles that set him back if he's hit). I have not seen any footage of you playing your brother, so this might not be the case - just a guess.
On the plus side, if you like fighting Link on FD, you can ban Pokémon and then go to what I think is possibly the second-worst stage for the MU on the Samus side while being comfortable on that stage. And being comfortable on your opponent's CP is a HUGE plus. (YS might be worse, since you die at like 70% to dair [or something really early like that], and still can die off the sides to up+B, even as you kill Link earlier... and he can take center stage while you are offstage and start walling, even though you have a platform to help avoid some of his stuff. I think BF is basically a slightly bigger YS and thus can sort of benefit ).
