Lileep is far from S-Rank. Being weak to Fighting-type moves is its biggest problem. Lileep is useless against nearly all Fighting-types in LC. No competent player is switching their Mienfoo into a Lileep in the early unless you're 100% sure it's going for a move that's not Toxic. During the lategame where Lileep has born worn down by weak hits and some residual damage, then that's the time to switch Mienfoo into Lileep so u can get off a Hi Jump Kick or grab momentum with U-Turn. Lileep sucks versus Croagunk, Scraggy, and Timburr, all of whom are on nearly every Little Cup team. Lileep is an excellent check to a variety of Pokemon like Murkrow and Water-types but it has a pretty significant weakness to Fighting-types.
Finally, Lileep has absolutely no offensive presence. Pokemon like Ferroseed and Bronzor are free to set up hazards in front of Lileep with little fear. Lileep is also DESTROYED by Toxic. A Toxic'd Lileep is a bad Lileep.
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Pokemon in this tier have very few flaws that are patched up by numerous positive traits.
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The flaws I've listed out are significant enough to keep Lileep out of S-Rank. Personally, I think Lileep may even be a B-Rank Pokemon. It's very good at what it does but its combination of 4ms, weakness to Toxic, and weakness to Fighting-types are a little too important for A-Rank.