At the end of the day Darkra was the ultimate glass cannon
Sceptile defeated Darkrai (who had healed with Dream Eater) 1on1 with 1 Leafblade
Pikachu tied with Latios
The other 4 were basically fallguys that did nothing while Tobias Pokemon relied solely on distance attacks. Both didn't take many hits to go down.
Ash was nowhere close to E4 tier and yet 2 of his Pokemon were equal to those 2 legendaries, meaning Tobias isn't E4 tier either
Had Ash brought his 6 strongest Pokemon with him and not a mix and match (seriously, Gible?) he'd clearly have done much better, especially based on Tobias doing so well solely by relying on the "Sleep-Dream Eater" combo for every battle shown.
When did he say "on par"? He said all the Brains were much stronger then Gym Leaders.
Ash beat every brain he fought, yet Lorelei, Agatha and Flint each destroyed Pikachu. Both Diantha and Adler wiped the floor with Pikachu too. He never came close to being equal to any of them he just got slaughtered. Then there is Infernape vs Flint's Infernape or Cynthia vs Paul's entire team which were all slaughters too.
Up until Kalos, the E4 and champs have always been portrayed on a completely different level then Ash and his Pokemon and semi-invincible, guys like Tobias and the Brains, all of which below E4 level were basically where Ash at his peak ranked until now.
Right now Greninja, even without transforming, has given the champ a run for her money. This is a feat of strength none of the other Pokemon have come anywhere close to accomplishing and puts both Charizard and Sceptile to shame
Just figured I'd comment on the second part of your post. Lots of good logic here, though! Quite comprehensive.
Regarding Pikachu's relative performance against the Brains and E4, it's not quite a fair measure of the Brains' caibre, particularly Brandon's. Pikachu KO'd a Regice that Brandon had literally
just caught - it had extremely minimal training by Brandon. The strength demonstrated by Regice once Brandon returned in D/P is a better indication of Brandon's calibre as a trainer. Regirock also took down Reggie's team with what appeared to be rather minimal damage, and Reggie had an equal amount of battle experience to Ash as of D/P at the time.
Greninja, without his transformation, did indeed manage to land that hit on Gardevoir. But that was a combination of his speed along with Ash's strategic thinking - using the smoke from the initial attack to mask a follow-up Water Shuriken, which itself masked a follow-up Cut. But Greninja landing that one strike in base form itself doesn't necessarily put Sceptile or Charizard outright "to shame". Sceptile KO'd a Darkrai that KO'd
every single Pokemon of all the Gym Leaders in Sinnoh - if we assume that ended up including Volkner, who himself is canonically capable of competing with E4 members (further implied by him not using Raichu against Ash), then Tobias' Darkrai is around E4 level. Plus, Sceptile took a direct Ice Beam from it and kept going, when neutral attacks OHKO'd Ash's other Pokemon. Base Sceptile is probably at least as fast (or even faster) than Greninja, given he chased down Speed form Deoxys, so landing a single hit on Gardevoir would likely be within his reach as well.
Charizard didn't really get a battle against a strong opponent as of its most recent appearance, so we don't know what the limits of its strength are with its training. But he took Iris' Dragonite's Dragon Rush with no visible damage, whereas that same move easily OHKO'd Dawn's Mamoswine. Charizard could probably also land a hit on Gardevoir - for one, he can evade her attacks with his flight, and his attacks likely have more raw power and definitely cover a wider range than Greninja's - just Flamethrower alone would torch most of the battlefield.