Shuckle is honestly probably one of the best walls in UU right now. Swellow really can't hurt him at all. Seriously, this guy takes hits a lot better than the Rock/Steels in UU plus it takes hits better than all the special walls there too. It can pose a threat to anything coming in by Knocking Off their item and it can also Encore their attempts to set up.
Swellow 3HKOs with Guts Brave Bird actually so it is not that great of a counter. It cannot hurt Swellow at all so if it switches in on Brave Bird it has two options, either take the second Brave Bird and Rest in an attempt to stall it out of HP or Encore Brave Bird to give something else a safe switch in. In the former situation all you are doing is giving Swellow an opportunity to Roost back up, which I don't see as that bad of an option on Swellow, especially if Shuckle is the best answer you have for it. The latter is pointless as anything that can take Brave Bird should be able to take anything Swellow throws at it, except possibly a random Hidden Power, and all you're doing is risking a death by CH for nothing.
Having said all that I've never had a problem with Swellow in UU as it is so easy to wall (and kill) with any Normal/Flying resist, particularly Rotom as it resists anything Swellow can hit it with and works well with Choice Scarf. Also there is nothing wrong with bulking up its HP and Defense a bit in order to take a few hits. I actually like your version of Scarf Rotom with a bulky-ish spread and the ability to take at least two Brave Birds.
Heh, it basically counters all the super-hard special hitters out there in UU even without Sandstorm, and even the physical ones get screwed over in some way or another.
List of UU Pokemon that easily deal with Shuckle 1v1:
Raticate, Nidoqueen, Nidoking, Persian, Primeape, Dodrio, Muk, Hypno, Electrode, Mr. Mime, Sudowoodo, Granbull, Qwilfish, Mightyena, Vigoroth, Exploud, Mawile(lol), Aggron, Sharpedo, Grumpig, Seviper, Crawdaunt, Banette, Chimecho, Absol, Glalie, Bibarel, Bastiodon, Purugly, Skuntank, Chatot, Toxicroak, Probopass, Froslass.
There may be more than that but this is at least 34 Pokemon that can either cripple and set up on Shuckle or just hit hard with a strong SE attack. In fact, Muk couldn't have an easier time against it as it can neither Knock Off its recovery nor Toxic on the switch in. In that list I have also neglected any Pokemon that Shuckle wouldn't ever switch in on due to their ability to OHKO after set up such as Rain Dancers, Swords Dancers and the like, as well as hard hitting Choice Pokemon such as Hitmonlee.
I'm not saying Shuckle is worthless, far from it, it has plenty of uses as you have already shown, I'm just saying that when you are slower than everything and have absolutely no way of attacking whatsoever you can be a serious liability to your team.