I really don't know what you do for work but the way you dismiss the level of knowledge and comprehension needed for so much of the hacking and programming as well as ignoring or just not understanding the power that a sudo hive mind like having shadow clones would be to programing, particularly to larger scale programs is sometimes very infuriating.  The overwhelming power that such programing skill would wield, would mean that, putting it mildly, Theo would be able to program at a level high and above that of a theoretical AI of the 2099's.  Probably far above that.  Not faster, but better.  His code would be far more art then bit lines.  His programing would be self reflective designs in place of long block script.  It also would have been nice to see him put any of that power into making movies, games, comics, and TV shows that progress his desires for the world.  Sending someone through an experience that teaches you by way of empathy and growth would have been more then a little helpful, and would have taken him what? 30 clones a day for 6 to 7 days to finish a massive game? With the same numbera 2 to 3 weeks for a TV show?

the power scaling feels.... very inconsistent especially when we talk about shadow clone jutsu and Tao/Agatha.  Yes magic is powerful but in the universe you selected (the mcu) magic isn't nearly that strong, infact I would say you over played it a few hundred times over.  Yes it's effects are incredible but only when you can gather that much power and have enough time and channeling ability to use said spells.  Thus far no matter what spells or how powerful they are Tao and Agatha have had no trouble with them, even though they really should have.  If they where honestly that powerful they would be brushing up against Lesser Cosmic entities.  In some versions of them this would be accurate, namely in stories where the world is full of near Cosmic entities, or where they are the "real" main heros of the story.  But neither of these things are even remotely close to the mcu version, it's so far off base its wild.  You portray Tao so strong she should be able to go toe to toe with most Dimentinal Lords, and Agatha seems to be able to keep up with her no problem.  It's rather grating at times.

You also constantly under play the value and power of shadow clones enmass.  The ability to fight yourself, while you watch yourself from 3 angles, while shadow boxing the action from 6 angles, 3 for each side, for 3 hours a day for... let's say 6 months.  Thats the base equivalent of 5.5 years of combat practice with just 11 clones.  Now let's say Theo does that with 4 groups, that's a base of 22 years of fighting experience in 6 months. Just 6 months for 22 years, and that's with out factoring in anything else, like how much more efficient and effective such a thing would be.  And best of all hebwould be constantly fighting someone at his level.  Which would grow exponentially as he improves.  So for a normal person to coach the same level of experience Theo would have after doing this for just 6 months of this would take at least 3 hours of getting beaten up a day for 5+ years, then they would need to go for another 5+ years with a new competitor, and then do it again and again for probably another 75 to 80 years... at minimum.  And ALL of that would only be if Theo was in a normal human body.  And All of that is just one aspect that he could be focusing on.  He could have 1 set doing combat, while another set does fire element control, while another set does magic programing mastery, while another set does engineering, while another set does languages, while another set etc.

Like really, really, really, really, really, really, really, really, really, really, underplayed that power...

Back to the body:

Theo is in a super adaptive, hyper strong, demigod body that has the innate potential to reach Lesser god levels.  And I don't mean the asgaridan wannabes.  I mean like f**king Celestials, and Hope Summers.

That is something I really do not under stand why you did that.  You under played Hagoromo's full bloodline/body and powers to an  absurd degree.  The man had more chakra then all the bijū but the original 9 tails (who was several times more powerful then the leftovers that get sealed into Naruto) and had innate chaka control skills high enough to leave even the best of the kage's in the dust, and that was without him having a teacher or functional training.  For him and his brother it was just natural, like breathing.  The dude literally took on a reality warping, plain creating, dimention hopping Godess and won with only his brother for backup.  To say that Hagoromo was strong enough to 1v1 a Celestial would be about right.  Those Sage balls, simple concentrations of all 5 elements with the 6th yin-yang suppressing their size and expanding their power each one was powerful enough to straight up delete the fake 10 tails at the end of naruto.  The man breathed them into existence around him... no real effort needed on his part...  assuming Hagoromo just got a free attack on the Celestial it should take tremendous damage even from just those types of attacks.

The body Theo was given vs the power output he displays is startlingly off.  It's very off putting.

I get that you probably want to say "He's 8!" But he's not a human.  He's a demi god.  Born with enough strength to take a tank shell to a face with out harm would have been more sensible then making him a weak as a normal baby.

There are too many characters.  We now have over 50 named characters and I'm fairly sure I've forgotten more then one.  I know many of these characters are from naruto/marvel but even still it feels like there are too many.  This is often times more of an issue with written stories rather then comics/mamga/cartoons/anime, becuase there are no distinct appearances to visually memorize.  I honestly feel that there is just too many when I have to go "wait, who? Have we met them before?" for more then one character.  This does not include characters you are 'reintroducing', but thus far you have never doen that despite probably needing too in more then one place.

As a character, Tao started off great, but honestly as her power has ballooned ridiculously and the fact that she is apparently immune to consequences has made her become rather unpleasant.  The more she's involved in a chapter past about 100ish the less I seem to like that chapter.  If you are going to make her such a bully but also introduce someone equally as powerful while keeping the MC as both her bully target and him super weak then you really should have used Agatha as a blocker/stopper for Tao.  For the last 50+ chapters I knew as soon as Tao appeared the MC would be bullied again in that scene.  It's long since gotten repetitive and boring, not to mention unpleasant.

Fury is, imo, given a bit too much of a free pass for some of his late story decisions from the others, and Theo.  I am aware that you made Theo a blabber mouth for him to be found by fury, but some of the other people would take exception to his (Fury's) actions (peggy, hank, Jarvis, more) and they would also take exception to Theo's decisions to kill so many people, and would want there to be a better way (they want to have my cake and eat it too!), especially Charles.  But we don't see any of this conflict, and I feel like we are losing some of the more interesting interactions as this keeps going.

Although this is something that happened very early in to story its still something that bothers the hell out of me, which is that Fury somehow knew about Tao, that, realistically would never happen.  Tao and the other sorcerers would have erased everyone's memories, they may have met, but Fury would not remember it at all.  If this is actually in one of the comics I would be absolutely floored. (I am prepared, but will still be disappointed.)

I may not have been very pleased with Theo reveling his origins, but you did corner Theo into it so I understand why the character did so.  The thing I will never understand even a tiny bit is why Theo would willingly give out chakra to ANYONE else.  The other people in his head I get, kinda, for some of them, but other people in said universe?  Not a chance in hell.  What the f**k would Theo do if Nathaniel Ess*x got a hold of so much as ONE cell of that DNA?!?!

And why would he even consider giving an upgrade to Tao who's so problematic already is honestly almost as bad.

This action, while empowering other characters, directly dilutes the MC's place in the story.  And that's bad.  There are a million and one other ways to power up other characters and this is definitely up there on the short list of stupidest.  Like ffs stableize a few xgen lines and add them to a new extra chromosome, then add a few more and a few from the inhumans, then a few things from an asguardian and boom! A 10 power wielding super human 20x more capable then Steve Roger!  There are literally so many options!  So why the f**k did Theo pick the one that will constantly give his enemies the most advantages?!?!?!?  The best/strongest skills are the ones no one knows about.

Like ffs WHY?!