This obviously suffers from Journeys/PWC power scaling issues and that we have not seen the past aces in proper form for a long time - a when we saw them at least a little bit, Greninja schooled Lucario, Infernape was stretching his muscles against legendary...so who is here to judge? It is reasonable that they have become even better when we last saw them in competition.
And giving this sorts of opinion, important question always is - do we compare them generally (like which Pokémon is the best against all thinkable opponents) or against each other (where typing plays a big part, even when they are pretty evenly matched generally). The former, general, approach makes more sense IMHO.
But I would say the average of opinions is pretty clear and as poll shows, this is the most balanced numbering you will get...
1. Pikachu - in his peak form. With Pikachu being ever-present, it is Pokémon who is the first one where we must take into account his form. Meaning not like regional form or something, but more akin to sports parable, even the best sportsmen prepare their condition to be at their best when the important tournament comes, they are not undefeatable 365 days a year - Pikachu being small mouse, at least that is the most reasonable head-cannon - must abide by similar rules. So he loses here and there against some Grapploct but when last 3 big tournaments (Kalos, Alola and PWC) had come, he was MVP and arguably has given the best performance of any Pokémon ever in PWC final match. So Pikachu in his peak conditon with all gimmicks is N. 1, unquestionably.
2. Lucario - because Mega, because Aura, because Steel typing and because defeating Cynthia's Garchomp.
3. Greninja - in his Ash-Greninja form which will hopefully see at least one last time. There is much debate how PWC team beat champions. But IMHO Greninja advanced so much, that it is the only Pokémon that would not only edge-off, but could even soundly beat two absolute aces (yes, favourable typing plays part , but his iconic speed as well) - Steven's Mega-Metagross and Diantha's Mega-Gardevoir (which he was close to even before Kalos League). The only thing that puts him after Lucario is less favourable typing in general.
4. Charizard - the first gimmickless Pokémon and rightly so. And the most obscure, since we have not seen him battle much lately, the most recent memory is schooling Iris's Dragonite. And also being overshadowed by Alain's and Leon's ones. But it is still battle-hardened, very experienced and proficient "air-battle" Pokémon who first defeated Legendary. It is hard to imagine him not doing anything that other Pokémon of Ash's PWC lineup did in PWC sans Pikachu and maybe Lucario. IMHO when I saw Lance's Dragonite being tank and taking all those Ice/Rock/Fairy attacks of Diantha's Pokémon, I though, yep - I would like to see this king of Kanto and Johto square it with Ash's Charizard. I would say they would be similarly matched, no gimmicks, fits Charizard's long experience and rivalry with various Dragonites and would be pleasure to see. (Very small hope "Aim to be a Pokémon Master" mini series will give us something like that).
5. Infernape - because Blaze and because you saw him dodge that Gengar's unwillfully released Will-O-Wisp? I am still little bit sad he was not used to soften-up Leon's Charizard or to put his overpowered Rillaboom, but Journeys' team deserved its spotlight. With that said, Infernape deserves his victory against some Legendary.
6. Sceptile - yes, yes, Darkrai - what would you expect me to say? But still, imagine him in his Mega-Form?
And yes - good doggo Lycanroc, Incineroar, Melmetal, Snorlax, Krookodile and whole rest of Journeys gang Dragonite, Gengar, Sirfetch'd and Dracovish could make case for one of the spots. But with all fighting more or less done, it is hard to say whether we will get any definitive answer from AniPoke. So it is here to be debated to till the end of times I guess.
But on the other hand, me personally would be very glad to see the BIG 6 in their top form to perform last one time (on any occasion).
