This is a gross oversimplification. Falling from winning 9 races in a row to not win a single one with a car that was firmly placed 2nd in the WCC and which his team rookie teammate won numerous races with is not simply natural change/decline. Getting beaten over one lap at 29 by a 37-year-old not known for his qualifying heroics is not simply natural change/decline. There is much more to this story.
Also, about that win in the Toro Rosso - probably one of the most overhyped wins in the history of F1. We have discussed this already here in the topic. That car was basically a Red Bull on steroids. It was a Newey designed chassis with a powerful Ferrari engine strapped to its back. Even Christian Horner confirmed that that car was better than the RB4 at that point. Just look at Bourdais - despite being practically nowhere during the entire season, he qualified 4th for that race. That weekend, the Toro Rosso was the car to beat. Yes, it was a very good first win from a young Vettel who kept it together until the flag. But it always amazes me how posterity treats that win like it was achieved with the equivalent of a 2021 Haas.
I really think it's just what others have mentioned - narrow operating window, when everything suited him, he was a beast, when things didn't suit him, he was more erratic (and his other weaknesses that I agree he has always had, became more pronounced)
I think the explanation that he "never had it", or "just isn't that good" is just as big of an oversimplification, when Vettel's performances against same teammates vary so much, from one year to another (eg. against Kimi 2015-2017). I'm fairly convinced that if you stick Ricciardo in the 2013 Red Bull instead of Webber, he wouldn't have beaten Vettel, but if you put Webber in the 2014 Red Bull, he probably would get much closer than he was in 2013.
As for the Toro Rosso in 2008. The car was obviously good, but it really only became a Q3 contender in the second half of the season, and it was then when Vettel started to really outperform Bourdais. So again - big difference in Vettel's performance once the car got updated (although you could also argue that it was Bourdais who underperformed, he was fast at certain tracks, but couldn't get a result in... Also due to some bad luck).
In dry conditions it was still far off Mclaren, Ferrari, BMW, maybe on par with Renault and Toyota. It was among the fastest in the wet in Monza, but he also outqualified Bourdais by about a second, and dominated the race. "Overhyped" I mean ok, maybe, but it's understandable, no? It was a first win for Toro Rosso and Vettel, it was entirely on merit, he was praised in the same manner Lewis was praised for 2007 Fuji or 2008 Silverstone ("maturity", while more experienced rivals were dropping the ball). And you know, it was sort of "arriving on the scene" moment.
The Mclaren was also a fast car during that quali session, so why didn't Lewis, the rainmaster and future GOAT do better? Well, he eliminated himself by trying to go on inters at the start of Q2, and then missed the best of conditions (while Massa, who made the same mistake managed to squeeze in).