You don't exactly have to be extremely powerful to be considered an S-Rank criminal. The knowledge Zetsu and abilities Zetsu had was what most likely labeled him as such. Being able to spy, collect intel unnoticed, travel from location to another while giving his intel to his comrades to turn the tide of a fight is probably why he was labeled as an S-Rank criminal.
If he were by himself and only relied on himself, then I doubt he'd be an S-Rank. He's one of those who's performance becomes more dangerous when working with others. Especially if they happen to be S-Rank too.
The society he has intel on and is able to spy on easily is the society that labeled him as an S-Rank criminal. Since he's a threat to them in particular. Again, not a threat to them by himself, but the fact that he has S-Rank comrades also has something to do with it. You can say that they carried him to that rank since I technically believe that too but I consider him to be like an S-Rank support.
He can travel quickly, spy without having others realize it, send messages and signals almost instantly between Zetsus (gather intel and instantly inform), catch others by surprise (absorb chakra and supply comrades with that chakra), and control others and potentially merge and control the land (BZ and how he merged with the land. If all he were able to do would be travelling using that m, then I doubt he'd say something like, "I'm the land itself". He never displayed this again so I guess I won't include it since it could be wrong).
You also have to keep in mind that several of the other Akatsuki members, if not all of them, were most likely labeled after becoming rogue ninjas or labeled based on the performance they've displayed while on the village. Zetsu, on the other hand, has only been recognized as a member of Akatsuki. They probably labeled him S-Rank because of how increasingly dangerous he is as a support to them.
EDIT: Holy Crap, I wrote an essay