When considering Serperior's checks and counters, a few Pokemon come to mind, most of which are offensive. Some examples include Braviary, Swellow, Sap Sipper Pokemon such as Sawsbuck and Miltank, and opposing Grass-types. But to me, the biggest counter to Serperior is Toxic Spikes. Since Serperior is often found running Taunt, it is difficult to status it without catching it on the switch. Because of this, Toxic Spikes are truly the easiest way from preventing it from doing most of its jobs: set-up sweeper sets lose vitality and are unable to sweep full teams and Leech Seed sets are unable to stick around long enough to disturb the opponent and weaken his Pokemon.
That said, while it would otherwise seem like an inferior option, my set's purpose is to handle Toxic Spikes which, in my opinion, are the best check for any Serperior.
Serperior @ Leftovers / Life Orb | Trait: Overgrow
Timid Nature | 252 SpA / 4 SpDef / 252 Spd
- Calm Mind
- Giga Drain
- Hidden Power [Rock] / Hidden Power [Fire]
- Aromatherapy
This set is sort of similar to Musharna's flagship set with Calm Mind and Heal Bell, but this one trades in bulk for immediate offensive presence. Giga Drain is both STAB and recovery which makes it the best option for any Calm Mind set. Hidden Power Rock and Fire are there for coverage, and you basically have to choose which type of coverage you would rather have. Since many Grass-types are very bulky, it can be of benefit to run Fire over Rock. The issue here is that with Fire, you are walled by opposing Fire-types such as Flareon and Torkoal. For this reason, I typically prefer Rock. Calm Mind is there for boosting purposes. Finally, the choice between Leftovers and Life Orb depends on whether you want more immediate power or survivability. Both are good in their own regards, though Life Orb's immediate power is greatly appreciated.
The main difference between this set and the standard one with Taunt (in fact, the ONLY difference), is the presence of Aromatherapy. Aromatherapy is a really cool move for a variety of reasons. First off, it handles status that Taunt could not otherwise handle. Did you switch into a Scald only to get burned? Problem solved. Did your opponent set up Toxic Spikes that you are unable to get rid of? Problem solved. I have run Taunt Serperior alongside Heal Bell Miltank, and while it seems like they make good partners, not being able to handle Toxic Spikes is a very large issue. In addition to being able to handle pesky statuses, Aromatherapy is a cool move to have on teams in general. Untimely burns and toxics against your team can mean the difference between winning and losing a match. Giving Serperior Aromatherapy is a cool way to get utility out of the set, even against teams where Serperior is probably not going to sweep.
Overall, there's really no way for Serperior to beat many of the Pokemon that check and counter it. Faster Flying-types are going to give it troubles no matter what you run. Sap Sipper Miltank is going to wall your set whether you like it or not, unless you want to sacrifice better coverage just to beat it. Status is always going to be the bane of Serperior, and running Aromatherapy on Serperior is not detrimental for its Calm Mind set.