Of each vanilla type pokemon (and the very few that are dual-types that really, really exceed in this department), what are the strongest Pokes of each type?
What I mean is, which Poke from each type has the highest IV set?
Actually, IV sets have nothing to do with a type of Poke. A Cleffa has the same opportunity to have the same IV set as a Mewtwo. There are no limitations.
As for what you are asking, it is hard to specify the "best" Poke of each type. It all depends on what role you are talking about. Is it the best physical attacker of each type, or the best special attacker, or the best defensive, the most versatile, etc., etc. It is much easier to identify the crappy Pokes of each type (i.e. Luvdisc, Delcatty, Farfetch'd, Absol, etc.) than it is best. That said, I will attempt my best to do so from a competitive standpoint. Since there are many dual-typed Pokes in the game, I guess the only fair thing to do would be to judge them by their Type 1. For instance, since Swampert is Water/Ground, it will be considered in the Water group (where it suffers) instead of the Ground group (where it excels). The only exception would be the Flying-type of course, since there no Pokes with Flying as the primary.
At any rate, here is the list:
Bug: Heracross
Definite no brainer here. Best. Bug. Ever.
Dark: Umbreon
Wins not only because of its versatility, but because Tyranitar's Type 1 is Rock instead of Dark..
Dragon: Rayquaza (Legendary) and Salamence
See Heracross for Rayquaza. Salamence barely edges out Dragonite for its speed and better movepool.
Electric: Zapdos (Legendary) and Jolteon
Zapdos get the nod over Raikou due to typing and better movepool. Jolteon would be one of the best Pokes in the game if it had a better movepool, but still wins out since Electrics in general are limited.
Fighting: Machamp
Hands down, mainly because Heracross is considered Bug for our purposes.
Fire: Ho-oh (Legendary) and Blaziken
Ho-oh has no equal. Blaziken wins due to its versatility. It can attack physically or specially, and do both effectively. Charizard needs help and Arcanine has crap for a movepool.
Flying: Dodrio
This type is limited to the Normal/Flying variety. Dodrio runs away with this. Best Flying-move. Best base Atk. Best base Spd. That is all that matters.
Ghost: Gengar
No brainer.
Grass: Celebi (Legendary) and Venusaur
Celebi, duh. Venusaur edges out Sceptile mainly due to the fact that it handles Sceptile's best moveset better. It cannot use Leaf Blade, but it doesn't need to.
Ground: Groudon and Flygon
Another duh with Groudon. Flygon's Type 1 is Ground and is a much better physical attacker with STAB Earthquake than special attacker with STAB Dragon Claw anyway.
Ice: Regice and Walrein
Regice narrowly beats Articuno mainly because of it being able to special wall so well and it doesn't have the Flying weaknesses that Articuno does. Walrien mainly wins by default since Lapras and Cloyster Type 1 is Water and not Ice.
Normal: Snorlax
Snorlax is not only the best Normal-types in the game, but arguably THE best Poke in the game (excluding ubers). That said, it almost loses out to Blissey if it wasn't for the fact that it can cause severe damage while Blissey cannot.
Poison: Weezing
Weezing's Trait is what makes it the best. While Crobat also is immune to Ground attacks, it also packs a weakness to Electric/Ice/Rock that Weezing does not.
Psychic: Mewtwo (Legendary) and Alakazam
You could make a case for Lugia and Deoxys-F, but Mewtwo has the offense that Lugia doesn't and has the defenses that Deoxys-F can only dream about. Mewtwo is too well-rounded for its own good. It still falls to Tyranitar and Groudon pretty easily though. Alakazam is the best only because of its HUGE movepool and its speed, making it more versatile than both Espeon (horrible movepool) and Gardevoir (too slow).
Rock: Tyranitar
Best. Rock. Ever.
Steel: Jirachi (Legendary) and Skarmory
No explanations needed.
Water: Kyogre (Legendary} and Milotic
It's Kyogre. This is the hardest type to really judge since there are so many good choices. Going strait Water though, it is Milotic, especially if it has the proper nature (ALWAYS Bold) and IVs/EVs. Swampert and Lapras get honorable mention. Gyarados would too if its movepool didn't completely suck.
That's about it. While each type can still be open to interpretation, that is basically the best of the best.