Modern rap fans often have a strong recency bias and "what have you done for me lately" mentality when it comes to rappers in the GOAT conversation. Obviously, dead rappers like Pac and Biggie are exempt from this.
Jay has essentially been semi-retired after 4:44(8 years ago) and his post 4:44 output has largely fallen under the radar(EIL and the Jay Elect album). And his features have been hit(God Did, What's Free) or miss(Sorry Not Sorry, Jail) too.
This makes a lot of modern rap fans dismiss Jay as "irrelevant" in the current rap world despite the fact that he's in his mid-50's and already made his mark years ago.
It's like the "Lebron" mentality slipped its way into hip hop and now people value longevity and staying hot forever over having a strong prime that rappers can live off of. Jay bowed out gracefully but these kids still think that the Future and Drake method of "feeding their fans"(which Jay used to do) makes them more relevant to the culture and, hence, "better."
On the flip side, Jay gets praised a lot by mainstream publications like Rollingstone and Billboard because he's the safest GOAT choice for many people. He's rich, married to Beyonce, isn't caught up in any real scandals besides the one that just got dismissed, has good business ties, and stays out of trouble. These same publications are starting to rally around Kendrick too for similar reasons.
So, when people get exposed to Jay constantly being deemed number 1 or top 3 despite his semi-retirement, it causes people to check out his work to see what the big deal is with him. And, sometimes, these fools will skim through his music(word to Renegade) and decide that's he's overrated and not particularly skilled or lyrical based on his crossover hits or bottom tier features like Monster, Swagga Like Us, and Pound Cake.
They don't get that a lot of Jay's greatest qualities are best exemplified on his B sides and deep cuts as opposed to his big hits so they'll base their opinion of Jay as a rapper from a very surface level angle and not see what the big deal is.
Tbh, Jay's most commercial music was always the weakest display of his rapping and music overall which affects perception from people who didn't grow up on him. He has his moments like Dead Presidents, Can't Knock The Hustle, 99 Problems, Big Pimpin, Hard Knock, Story of OJ, and Song Cry where he balances lyrical prowess with commercial appeal.
But then you have commercial songs like Ain't No Nikka, Change Clothes, Hey Papi, Jigga That Nikka, Sunshine, Nikkas in Paris, Holy Grail, Empire State Of Mind, 03 Bonnie and Clyde, Excuse Me Miss, Guilty Until Proven Innocent, Show Me What You Got, DOA, Young Forever, Things That U Do, I Know What Girls Like, Holy Grail, and Tom Ford which REALLY don't do Hov any justice when it comes to showcasing his best qualities as a hip hop artist. And casual rap fans who don't listen to his full projects will base their opinions of him off that too.