It should not be Rhodes, either. I notice some toss out candidates for Avengers leader in the era of Wilson as Captain America, yet had no problems accepting a recently resuscitated Steve Rogers being picked to be the Avengers' leader during that phase. If anything, Wilson has more modern-day experience (at the point of stepping into a leadership position) as a superhero (blended with his work in the military ), as he's of this era and did not have to play catch-up like Rogers, yet here we go with just about anyone offered up as the new Avengers leader other than Wilson's Captain America.
Why? One of the weakest part of the MCU's version of Spider-Man was reducing him to some teen sidekick, running around yelling "Mister Stark!" with hardly any of the self-reliance (and none of the sense of sacrifice) of the original character from The Amazing Spider-Man comic book. No one needs to see yet another film with Spidey-Lad and his hero-worship issues about the dead Tony Stark or some variant.
What you're saying is just do write anything to drag Stark back into the MCU. Doom is not Stark, and for his 1st appearance in the MCU, he should be a distinct character, not some variant of a dead man.
Unnecessary, unless you believe moviegoers are so simple-minded that they need a forced connection to explain why the same actor portrays different characters in a series. As distinctive as the late Charles Gray was in appearance, no moviegoer needed 1971's James Bond film Diamonds Are Forever to justify why Gray's Blofeld resembled Gray's Dikko Henderson from 1967's Bond entry You Only Live Twice. The reason is that audience of that period were mature enough to accept actors appearing more than once in a series as different characters having no connection. It was not a problem in the Bond example, and it will not be a problem with RDJ's Dr. Doom.
I do think Rhodes as leader does have one issue and that is he was replaced for who knows how many years by a Skrill and I also think WIlson will earn lots of trust in the upcoming movie so I do think you might be correct in that he is best choice as team leader. I do wonder though were Nick Fury plays in all of this. I mean he is still around as well.
As for the debate of Thor coming back. Not sure it is a lock because of some of the conflicting statements said by the actor. But yep I think when push comes to shove he will also return . I do think they will address some the actors issues about how Thor becoming to comical and I guess try and go for a better balance. I also think Banner will come back as traditional Hulk and not Smart Hulk.