Since the most recent patch probably didn't affect the best characters in the game, I think it's time to ask the what I think is the most important question in the meta right now. Who fights Sheik, ZSS and Rosalina the best at the same time? These character are probably now set in stone as the top 3 as of now. If a character loses out to one or two of them, they won't be making many top 8 at majors anytime soon.
From all of my experience, and I'll be very honest about this. This has always come from my experience, but...
It's Link. You might already write this off as a troll post, but hear me out as to why I think this way in the first place, you shouldn't pass this up just yet.
Link doesn't have the best mobility in the game, nor the best frame data or anything like that, but what he lacks in mobility and some attacks having sub-par frame data is literally everything else. Link has a Jab > Spin Attack combo against the three characters, which is basically a kill confirm at higher damages, Link has the ability to out-range all three characters in terms of attacks and Link has, above all else, projectiles that are actually reliable against these opponents and kill power.
First, I'll talk about ZSS, since I know more about MUs for her and Link than I do with the other two.
With Zero Suit Samus, she's actually the least troublesome of the three queens for Link. ZSS has the best mobility for sure and great attack speed and combo-to-KO ability, but what matters here is how Link retaliates. If ZSS is going for her U-Air ladder, Link needs to first DI and then perform one of 3 options, F-Air, D-Air or N-Air. The least damaging, but safest all around, is using his N-Air on her to possibly reposition him from disadvantage to advantage. The second most safest is his D-Air, which he has to literally fast-fall with at the right moment in time to turn it around. If ZSS whiffs her Up B and Link performs anything to get him out of stun, Link can fast fall faster than her to get himself into a punish position quick; the best way to do this is using Link's N-Air and avoiding ZSS. If ZSS uses her Flip Jump, another example, wouldn't it be wise for Link to actually stay in the midst of it and hit her near the end with an upwards attack?
Secondly, Link has something against ZSS that ZSS doesn't have against Link, a very great ranged get up option with F-Air, and range itself. And from that we also have Link's range vs ZSS's range, which is actually superior even with worse frame data. While it's true that ZSS does have a great projectile, it's not the best and can easily be trumped by Link's N-Air or Bomb. Link's Bomb also allows for setups that are unimaginably amazing against ZSS. The Bombs need to be respected, especially paired with Link's Boomerang, which makes the Bombs abnormally better since two items cover the field of options.
One thing that people often overlook is Link's ability to actually defeat ZSS's recovery options and even kill ZSS vertically. Link can beat ZSS's own Flip Jump with an F-Tilt or an F-Air if ZSS uses it parallel to Link at the perfect range, so if ZSS gets hit, it might potentially be all over at the right damage. If ZSS goes under the stage, Link can RAR N-Air, B-Air or even D-Air her into a stage spike (and only on Battlefield can he stage spike her with a grounded Spin Attack).
With ZSS, it's a game of patience and accuracy, as well as knowing when to dodge her grab, because that's the thing that will sometimes get me, so if I see her rushing up and going for the grab, I'll immediately roll away for safety and punish accordingly or QDJ (quick double jump) away from her and then punish. Accuracy comes into play when Link has to make sure every hit counts and that any hit on him can spell disaster.
Stage selection also comes into play with this, as selecting Final Destination and Lylat Cruise are Link's best options against ZSS. Final Destination won't allow ZSS to kill much earlier and Lylat Cruise has a large vertical ceiling, making it similar to FD in terms of usage. These stages also allow for Link to possibly gain the upper hand in battle, since the removal of platforms for FD means he can freely FF D-Air for a potential punish, and the low platforms in Lylat means that Link can safely hit ZSS from underneath with somewhat little repercussion, especially if Link pressures with U-Tilt and ends the pressure with U-Smash.
In my experience playing ZSS, Link vs ZSS would be a clear 50:50. What does Link in though, is the fact that he's heavy, has below average speed and has some somewhat below-average moves in terms of speed. Otherwise, Link has the tools to at least fend off ZSS. And remember, this is from my experience in offline tournaments and With Friends, not For Glory.