Comparing the 90's SPIDER-MAN, which ran for 5 seasons and 65 episodes (the second longest run of a Marvel cartoon, least if you discount the fact that the 60's Spidey show would "recycle" episodes to boost their numbers) to SS-M sometimes verges on ungrateful, especially after a mere 2 episodes. Simply by debuting in 1994 and being the second big Marvel cartoon of a generation, right after X-MEN, SPIDER-MAN: TAS has earned it's place on a Top 10 Comic Cartoons list. It was a trend-setter. Even Sam Raimi's movies took some plot & character details from that cartoon, especially in SPIDER-MAN 3. It aired for ages on cable in reruns. It earned millions in merchandise.
Of course, those who are seeking to compare the two point to the one area that SS-M is already superior in; animation. The pilot of S-M:TAS was it's animation highpoint, and even by episode #2, the animation quality was not on par. But S-M:TAS really didn't start suffering from glaringly bad animation for the time until about the middle of Season 2, and by then it was in free-fall. Part of the problem was of course Marvel being a smaller company than it is now, and the comic-bubble burst by 1993-1994; by 1995-1996 Marvel was bleeding. But the other part was the character models were too complicated; often overly muscular and all that. In contrast, while some people feel that Cheeks Galloway's character models for SS-M are "too cartoony", they are simple and animate very well. I mean, that was what made B:TAS so good to look at. The budget from Sony is probably larger, too. And animation techniques have improved since 1998, when the 90's show ended.
The 90's show is better remembered not for the animation, but for the writing quality. It embraced the notion of a storyarc better than any cartoon of the time and even better than many since. Every episode (or almost every episode) was a cog into a larger story and every element was revisited, even wonky ones like The Spot's dimensional machine or Baron Mordo & Dormammu. Despite being crippled by an oppressive censor-board, the show had thrills and chills, and some solid writing and acting. That said, while John Semper (the Timm of that show) blames all of the show's flaws on the animation, editing, censors, networks, Avi Arad, etc., and while he is over 50% correct, some ills were all on his watch. Sometimes some storyarcs dragged a bit long, and some other seasons lacked focus; Season 4 in particular. Too many episodes were wasted on Morbius. Why Rocket Racer, Big Wheel and The Spot were granted full episode status is a mystery. Dr. Octopus spend most of his time as a Kingpin flunkie, which is underwhelming. Semper's utter disgust for Hobgoblin, a rogue forced on the show by a prior writer, caused him to ruin the villain's exit despite the fact that Mark Hamill and even Semper himself managed to write him as a shrewd, cool rogue. Part of SECRET WAR simply didn't work. And the show ended on the mother of all cliffhangers and even a decade later Semper doesn't feel that Peter needed to be reunited with MJ. And by the end, the animation was choppy, the editing ridiculous and they invented the NARUTO angle of overplaying flashbacks to save animation dollars. Even without punching, many of the fights were paced poorly. You can actually storyboard a fight without one punch if you are good enough. They weren't.
SS-M also has the benefit of hindsight, just like I do in noting all those flaws. The 90's show only had the fluff of the 60's-80's to look at, which was hardly helpful.
Still, newer models can outdo old ones even if the older ones broke ground. The Mustang didn't predate the Oldsmobile but most would say the former was better. Nostalgia for the NES or Atari 2600 aside, video game systems and games have improved greatly since. And in some ways shows are the same. S-SM has a good budget, solid writers, good storyboarders, a less oppressive censor board, and the hindsight of having not one but THREE prior cartoons within the last decade to examine to see what worked and what didn't (SPIDER-MAN UNLIMITED providing much of what not to do).
Could SPECTACULAR SPIDER-MAN evolve into a better show? If the show is capable of shifting moods; getting dark or serious if the story requires it, then I will say yes. But in way, it can thank the 90's show for being able to do so.
Admittedly, I haven't watched the 90's show in years. Part of me dreads that it was good for the time but hasn't aged well at all.