I think the Ascians for sure frequently underestimated the resilience, resourcefulness and intelligence of the sundered. I don't think you're wrong there. It's a common trait in "mastermind" villains, and such arrogance is more often than not what leads to the downfall of such characters in the majority of stories they feature in. But I'm not inclined to think they threw that in amidst other qualities the sundering did have an effect on just to illustrate Emet-Selch being an ass, lol. I mean, the Scions are comprised of some of the brightest minds in Eorzea, and as Vyreus pointed out it took an entire group of them plus the strength of possibly the most powerful/ skilled warrior living to collectively overcome a single Ascian who had maintained a large degree of his powers, and even then it was close, even if they did triumph in the end. The only Ascian we have come close to defeating in a one-on-one battle has been remarked upon as being severely cracked and weakened from years of body-hopping resulting in a steady slide into insanity (...or an alien space rock, if you buy into that.)

Though for the record, I'm also not asserting there's a clear boundary between Ancient intelligence and sundered intelligence - I imagine there's an overlap at the extreme ends of both spectrums, nor am I suggesting that higher levels of intelligence automatically correlates with the ability to apply it effectively. It's no secret smart people can be really dumb; such intelligence isn't an adequate substitute for emotional intelligence, common sense or poor judgement, which we can often see in the real world, and I don't think the Ancients are any exception to that. Some of the quests in Elpis demonstrate this pretty well.

As for Emet-Selch, I think what pissed him off regarding the sundered isn't their inability to reach technological milestones (especially since as you say, such progress was frequently trashed by their side anyway) but the way they allow their base instincts of greed, selfishness, malice, and violence to dictate their actions and create widespread destruction and tragedy. It's basically anathema to what the Ancients believed in and how they operated, so his disdain isn't really surprising.