Whichever starters had Mega Stones. Kidding, I know all six of em do. (Thx, Alpha Sapphire and Omega Ruby.) Before my answer, I've got a list of the pros (maybe cons) of each partner.
1) Venusaur - We're going by Dex Order, so there's no bias in the listing. Now that we're talking two generations spacing, you can actually get away with the Sunny Day/Solarbeam combo. Leech Seed, Poison Powder and Sleep Powder are great for defense. Synthesis does Venusaur justice. Not as defensive as Blastoise, ot as offensive as Charizard, but at least it can drain/heal.
2) Charizard - Charizard can use Fly, unlike Gen1. GF had the common courtesy to do what they conveniently forgot to do in Gen1; adding Wing Attack upon evolution. Aside from its awesome attacks, such as Slash and Flamethrower, there's nothing left to note about the beloved dragon, despite the fact that it's a Fire/Flying.
3) Blastoise - Decent in defense, what with Withdraw and Skull Bash. Among the few changes from Gen1 would be the notable type change in Bite.
4) Sceptile - It looks like a tradition in Grass types to have decent defense. It learns Fury Cutter and Leaf Blade, and was the only Pokemon to have Leaf Blade to date at the time. I'm fairly sure Sceptile has more defense than Blaziken and more physical offense than Swampert.
5) Blaziken - Congratulations, GF, for having revived the dual-type starters. (Although not all my favourite starters have two types.) Blaze Kick AND Sky Uppercut!? Are you kidding me? We really went to the age of endless devastating moves by the Third Generation? Both moves have 85 Power and 90% Accuracy. An excellent contender, despite the fact that it has the lowest Defense out of Hoenn's starters.
6) Swampert - Move over, Quagsire. Swampert has Muddy Water and Earthquake, which makes it quite sturdy. It may be 50% useless in damaging Charizard, but that's just Mud Bomb and Earthquake. Muddy Water'll put it in its place. (Wing Attack and Fly, tough as they are, don't expose any weakness in Swampert. Thanks, GF, for not making Ground weak against Flying.
I think both sets of staters are equally effective. Tie game, folks. Venusaur would beat Swampert, but lose against Blaziken. Blastoise would beat Blaziken, but lose against Sceptile. Charizard would beat Sceptile, but lose against Swampert.