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Since Scolipede can learn the exact same moveset as the Ninjask for a baton pass role and it's bulkier, wouldn't it dominate Ninjask as a Baton Passer 99% of the time?

The only time I see Ninjask being better is if Sticky Web is the only trap on your side of the field. Ninjask is unaffected by SW whereas Scolipede will suffer from it if it's not RS'd yet.

Partially asking this because I'm trying to decide whether or not to use Scolipede or Ninjask as a baton passer.

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In general, you are right. Scolipede is a lot bulkier than Ninjask so might be preferable as a Baton Passer. It also isn't 4x weak to Stealth Rocks, which is definitely a bonus.

The only situation I can think of (aside from the Sticky Web you mentioned) where Ninjask might be preferable is if it is necessary for you to move first on the first turn. Scolipede is pretty fast, but Ninjask is the second fastest Pokemon in the game (just slightly behind Deoxys-S), so will move before all non-scarfed opponents (priority excluded, of course). Of course, Scolipede can just Protect on the first turn if it wants to make sure it is faster, so even this isn't a particularly great advantage.

So, in short, I think Ninjask is pretty much outclassed now.

To add insult to injury, Scolipede also gets access to some entry hazards (it can get both Spikes and Toxic Spikes), making it a potential all-round utility Pokemon. It also gets a powerful STAB move, Mega Horn, which is something else that Ninjask lacks, although since it is a Baton Passer it doesn't really need it, but still it is something else to note.

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Very true. Will probably be making a Scolipede now lol. Thank you!