De-aging VFX is not that cutting edge, Lola VFX has been doing that for a while. First in X-Men 3 (with uh dubious results) and then much better in Benjamin Button. But yeah it's the most impressive part of their movies probably.
And I'm sorry, but it's not just 30 seconds. BP suffers from a lot of greenscreen/compositing issues, and Spiderman's suit in Homecoming looks fake pretty much the entire way through, as does any time we see a head poking through a CGI suit in other movies, notably Iron Man and Bruce Banner in Infinity War. These are main characters we're talking about. And in this regard, the way Alita mixes CG elements with people, it's just on another level. And in this particular aspect, yeah the CGI in Marvel's films is awful.
Overall though the VFX quality in Marvel's films is fine, just not particularly noteworthy or praiseworthy to me. *shrug* You bring up Academy Awards as an arguement point, but if their visual effects are so great how come they haven't won a single time in this category after over 20 movies?
Alita has some noticeable compositing issues in the same way with some faces in the Motorball scene or Hugo in his final scene and again, you are generally cherry picking a handful of shots which is easy to do when taking from a 20 film filmography. And the most egregious offenders that people tend to bring up, like Black Panther or Bruce Banner in Infinity War are scene that were reshot and/or had late changes in editing/post production, which isn't exactly a fair 1:1 comparison with shots that were planned and prevized from before any actors were ever shot. There is even a clear difference between some of those shots and others in the Marvel films alone.
Also, I don't know if you noticed, but that category is pretty competitive and many winners get to boast of doing something ground breaking. I'm sure that if you set aside your bias, you'd acknowledge that even getting nominated puts a film into a cut above "average", and in the same class with losers like District 9, The Dark Knight, the Planet of the Apes trilogy, Prometheus, Max Max:Fury Road, The Revenant, The Martian, etc. You know, movies that are just "fine". I believe they'll take a win this year due to the hype surrounding Thanos in IW and not a lot of strong competition.
Marvel/Disney never bothered pushing their movies this hard with the Academy before, usually this is a lost cause. Heath Ledger had to die for one of his greatest performances to be recognised by the Oscars because it was a Batman film.
Yeah, to my knowledge, this is the first time Marvel has ever bothered to have an Oscar campaign at all. It also seems like the Academy is a bit adverse to awarding straight up "blockbuster" action films and franchises unless there is a lack of anything else.