Haven't viewed this post in a while, but last time I checked there was a strong argument stating that Baton Pass needed a nerf because of its over-centralizing effect on stall teams. Baton Pass is generally considered too powerful against stall teams, which is why it is in need of a nerf.
If this truly is the reason we are nerfing it (not because we dislike it or think its cheap), then we need to focus on making it weaker against stall specifically. This is my suggestion:
Ban the use of Ingrain on Smeargle. This has been done before in gen 3 and was a great way to reduce the effectiveness of Baton Pass chains then.
Why it works to make Baton Pass weaker against Stall should be rather obvious. Without Ingrain, phasing is a reliable way to beat Baton Pass teams. Now, before you go on and complain about Soundproof or Magic Bounce, please hear me out:
Currently Skarmory, Hippowdon, Mandibuzz, Snorlax, Sigilyph, Volcarona, Aerodactyl and Crobat are all viable users of Whirlwind (some of the latter may not be the best options on stall teams however, so lets focus on the first 4).
Skarmory, Hippowdon, Mandibuzz and Snorlax are all great stall pokemon and great users of Whirlwind. Their only counter on a Baton Pass team is Espeon, who can reflect their phasing. However, each of these Pokemon can beat Espeon in a 1 on 1 situation because they are physical attackers. Espeon cannot stay in to Calm Mind and will eventually die to powerful physical attacks like Brave Bird, Earthquake, Knock Off, and Return. The end result is that mispredicting a few Whirlwinds with Espeon, will quickly lead to a dead Espeon and the Baton Pass team is defeated.
Ahh, but you Espeon can setup against any of the above after a few Defensive boosts! ... So why does Espeon have defensive boosts? Leading with a phaser gives you a huge advantage against Baton Pass teams, if they try to boost, you phase them. If they try to Baton Pass to Espeon, you hit Espeon hard. The match is no longer an auto win, its a skillful mind game that both teams are involved in. If you let Scolipede get boosts, you will be in trouble, so you need to play smart and phase early and often.
Lets look at another great option for stall teams, Red Card. Currently Red Card is best used on Sturdy users like Foretress, Donphan or Skarmory, all of which are gladly placed on a stall team. Now typically Red Card is rendered useless because it isn't activated when you get 1hko and Ingrain prevents phasing anyway. But, without Ingrain, Stall teams and reliably beat Baton Pass. Now, before you go on and complain about how simply phasing a team resets them and doesn't beat them, please hear me out:
Seismic Toss and Nightshade are both common moves on stall teams. They are able to deal significant damage to all Baton Pass users except Vaporeon. Simply spamming Seismic Toss will force the Baton Pass team to take significant damage while acquiring boosts. On the special side, setting up 3 Calm Minds requires Sylveon to take 3 hits at least (assuming you used Vaporeon to pass a sub and protect it on the switch). Another 2 Calm Minds can be acquired from Espeon or Mr. Mime. Now, the Baton Pass is ready to sweep, despite the majority of its team being at relatively low HP. Assuming you need at least 3 Calm Mind boosts to reliably 2hko Chansey, Sylveon and Espeon are probably relatively low health. Now, if you introduce the idea of Red Card at this point, the game is easily won. Sturdy survives the Stored Power, phases the team, and now they must start again. This time, they cannot beat the Seismic Toss / Nightshade spam. Specially, they cannot get enough special boosts to be able to defeat Chansey or Blissey.
Lastly, we should give special mention to Deo-d, who can work well on stall teams. The combination of Knock Off / Seismic Toss + Taunt is a great way to shut down Baton Pass teams. If they switch in Espeon, they will face dying to Seismic Toss before they can Calm Mind enough to kill Deo-D. If they switch out, they face being Taunted. Once Sylveon or Vaporeon is taunted, the stall team can switch to a defensive counter, and start playing aggressive (i.e. putting down hazards or statusing the threat, specifically Sylveon who can hurt Deo-d with Hyper Voice). At this point, the Baton Pass team will likely switch out, to which you ultimately bring back in Deo-D and repeat the process.
In conclusion: If you want a simpler solution to nerf Baton Pass we need to solve a simpler problem. If Baton Pass is overpowered because of its unfair advantage against Stall teams, we should focus on making it weaker to Stall teams. This is most easily done by following the precedent set in Gen 3, and Banning the use of Ingrain on Smeargle. This allows Red Card and Phasing to be used in conjunction with Seismic Toss and Entry Hazards to beat Baton Pass. See above for details.