Honestly, it's hard to say because there's no solid information, at least not much, and what we have is vague statements and those filtered through PR talk, or people who don't know 100% of the story. Anyone who does, is unlikely to tell in an unbiased fashion.

Both bring up good points, so I'll say this:

Joey Q is no Jim Shooter. Jim Shooter gave a golden age of storytelling. We had the X-Men, their spin-offs New Mutants, Excalibur, X-Factor, Alpha Flight, and the minis under him like Magik, Kitty Pryde and Wolverine, Longshot, Firestar, Fallen Angels etc. that really made them stand out. We also had the Avengers, one of the best runs, by Roger Stern. We had Spider-Man, who remained a very strong title in this time, being both independent yet connected to the world thanks to Stern, Tom DeFalco, and David Michelinie. We had Daredevil by Frank Miller, Thor by Walt Simonson, Fantastic Four by John Byrne. We had lesser titles like Power Pack, Cloak & Dagger, Rom: Spaceknight, Squadron Supreme, Moon Knight, Power Man and Iron Fist, West Coast Avengers etc., all of which were beloved and long-running despite not reaching heights like the others. Hell, even Iron Man had his best run here, a character not known for being able to hold his own. Some of the best storylines, like Days of Future Past, Secret Wars, Born Again, Kraven's Last Hunt, and so on, came from his tenure.

He helped to create a great, interconnected continuity that really was a living, breathing world. He also pushed the boundaries of what could be done in the superhero medium, striking somewhere between fun and bright, with dark and mature, without fully committing to either one in a great balance. Finally, Shooter acknowledged that some titles aren't going to sell as well as others. Rather than can titles for not performing on par with X-Men or Spider-Man, or whoever he wants to be big, he focused on making them good to the people who were buying those comics, because ALL comics are needed to stay afloat.

On the other hand, Joey Q has always been about enforcing a specific vision regardless of how bad it was for others. He didn't care. He forced OMD to happen for himself, and no one else. He's also not the biggest master of continuity either, considering the mistakes that began to pile up with him (look at Civil War -- no writer was apparently on the same page when making it). He also did dumb things, like he introduced X-23 from the cartoon and into the comics which is good... but made her a teen prostitute for edge factor, which is bad. Likewise, when the mutants were suddenly shrunk and hampered with restrictions, I don't think it was something the X-writers specifically wanted. Just like when the Inhumans push came to be. I don't think the people writing X-Men were eager to have Inhumans intrude, or be forced to write the Terrigan Mists as being lethal to them, or constantly be sidelined the way they were. Writers have limits they to work with, sometimes very defined and intrusive.

Furthermore, Marvel has made long-term plans. The Inhumans push was a big plan to get their own mutant equivalent MCU ready, not anticipating they would be getting the actual mutants later. Likewise, the Avengers weren't a "small title" by any means, but their push to the center of the Marvel Universe with three consecutive stories and being made into Marvel's Justice League in time for when IM1 came out... I can see that they had this in mind. Spider-Man and Wolverine gave star power to the title, which is why they were there. Jack notes how Michelinie wrote the definitive Iron Man run before Spider-Man, and didn't have them interact even when he feasibly could've made it happen. That's telling.

I don't think that they had a specific idea of what the MCU would become, nor did they plan to completely exclude the X-Men and Fantastic Four on the level they did after 2012 up to 2019, but I definitely get a sense they were pushing the Avengers from a collective of lessers to Marvel's Justice League for a reason. My overall view is that this wasn't a "master plan", because no one can predict the future on the level that they could predict the MCU would be a media titan, but things were put into place for the MCU as it was being developed, and they increased as they went further into it, culminating with the X-Men and FF's blacklisting from media and sidelining in the comics after the Avengers movie.

They couldn't plan for the MCU to take off the way it did, because it could've easily backfired, but they did have a sense to try it out, and escalate as they got more successful. It's telling that suddenly the X-Men and the Fantastic Four are important and great again after the Fox buyout. Hell, we're getting a big X-Men/Fantastic Four crossover mini, which I doubt would've happened a few years ago.

That's my take.