Probably going to ruffle a few feathers when I say this but outside the first issues of the Ultimate Comics of the Ultimate Spider-Man series, Ben was never much a character in the comics. In Amazing Fantasy #15 Ben was like in one or two pages in that whole issue. Beyond he wasn’t really much beyond being Peter’s loving uncle that he indirectly ended up killing. Besides, Ben got plenty of focus in the previous movies(especially the Riami ones which were to their determinant in some ways). So why not take a new angle with this character? After all, there’s plenty of issues of Spider-Man where Ben doesn’t even get so much as a namedrop because they know they’d be beating horse. Why not explore the core Spider-Man theme of loss in a new way through this surrogate father-son relationship between Tony and Peter?
Ben always existed as motivation fuel for Peter. He doesn’t really serve much purpose beyond that. This is the MCU Spider-Man, and Ben is already dead and gone when we first we meet this iteration of Peter. Peter alludes to Ben’s passing when he explains to Tony his reasons for doing what he does when they first meet Peter isn’t going to be wallowing in grief over his deceased loved one forever. Tony Stark is his most recent mentor figure that has had a huge impact on his life. He’s had time to grieve Ben, Tony is a emotional wound that’s still fresh in his mind. Tony is the one character most audiences care about. Much like Peter in-universe; audiences are sad to see Tony go. I remember seeing eyes well up when Tony died. Peter mourning Tony Stark is going to have a lot more emotionally resonance to the most the MCU-watching audiences than him mourning a character who died off-screen and in the context of the MCU they have no connection to. Especially since the audience has seen way more of Tony than they ever saw of Ben Parker who generally dies off pretty early at the start of any Spider-Man story so I think it makes sense to place a greater importance on Tony than on Ben.
Couple of things...
It's a good thing we have differing opinions and views. Can you imagine how boring this place would be if everyone agreed all the time?
The important point about the Ultimate Spider-Man comics is that it DID make a point to show how important Ben is to Peter. Bendis went into sufficient depth about Ben and his education to Peter about responsibility. I don't have the best memory about the Ultimate line so I can't remember specifically if Ben was brought up again in later issues. But it didn't have to. The first few arcs made it perfectly clear about the importance of Ben and his impact on Peter.
Even in 616, the main continuity, Ben was referenced at times outside of the initial stories. The first one that comes to mind is issue #33. One of the greatest Spider-Man stories of all time, comes as Peter is entering college and makes a point of showing Ben and what he instilled in Peter. Again though they didn't have to show Ben in every issue because they made it a point to show his influence initially but would still continue to make the occasional reference when the story would call for it.
MCU Spider-Man has skipped this entirely. And not directed at you but for the umpteenth time this does NOT mean having to show the origin again. Showing Ben's importance or influence doesn't need to include showing him die, yet again. I'm happy they skipped the origin. However all Ben has received here is a brief mention. Twice. And not one person has said his name. For what is arguably a very important part of Peter as a character, they won't even say his name. Imo this is inexcusable. What's worse is they've replaced him with Tony.
I've argued this before but imo I think the MCU version of Spider-Man would've been different had he been available to their universe from the get go instead of having to be inserted later. With Spider-Man coming into an already established continuity they had to make certain choices to make it work. Otherwise I think the Tony thing wouldn't have been utilized.
I don't disagree with having Tony as a mentor. It makes sense in this regard for Peter to look up to him. But two things. Peter doesn't need to be so clingy. He can still be a competent young guy without having to rely so much on a mentor. And you can still play the mentor card while paying respect to Peter's first and most important father figure.
While I can accept certain changes, this one in particular is difficult to get past. I dunno, maybe FFH will sort of make up for this flaw within Homecoming. We'll see.