Yes and no, that's how I feel about most of your points at least.
1. H.E.R.O: It's true, there's not much of a choice to avoid H.E.R.O, but your missing a big point. It's mentioned that it's only a matter of time before Superhumans are identified and added to H.E.R.O's ranks. But they are still working things out. Dexter even mentions with the release of the MC's identity reveal, they'll have to push back their time table, which we know is in reference to their debut to the public. I don't think they have the time to worry about us, which means someone is influencinv our capture from the inside. My guess is Deus, which brings me to the next point.
2. Escape: It's possible like you were says, from an outside source, but that source isn't going to take out Deus or Nicolette, too strong, and too end game. It would most likely be Ella's pets, either Valravan or someone else, but NOT Goliath (she mentions it's not time yet, definitely endgame), and NOT herself (she's not that nice). As you mentioned, Deus wouldn't free us, he probably already knows how it'll all play out, so I wouldn't be surprised if he didn't even know we even got to H.E.R.O in the first place.
3. The Leak: Ella didn't do it, calling it now, her MO is ALL about subtlety, imagine if our UNDYING LOYALTY is tested and we reveal everything we know about Ella. Publicity is not in the cards for her, she wouldn't leak us. I honestly don't know who, but I have a gut feeling it could be Deus for whatever plan he's concocting. There's literally only a hand full of people who know who we are, not even CLARK or any of his subordinates that we know could identify us at the College face to face on serval occasions, so I doubt that it's someone we haven't seen yet. Deus is the only variable that has shown to know more than meets the eye, and work for his own agenda despite affiliation (i.e helping Valravan, Dexter mentioning he's not Zack and will be the death of Xanthe, or something along those lines). Tiffany wouldn't, we are her only ally outside of her Father's influence. And Ella is, Ella, despite what she does and says; I trust her more than I do Deus. Deryl no, nothing has indicated that, and Jake is a variable that Weird World will cameo at endgame in my opinion, water under the bridge, if you even let him live.
4. H.E.R.O Foreshadowing: You're looking way too deep into it bud, this is a porn game, not Attack on Titan, our dad isn't Keith Shadis (unimportant character foreshadowing). The MC's Dad is more of an informant if anything than some criminal mastermind who planned to send his son to a next big thing superhuman college. Let's look at the facts:
A. He picked the College because it's the best in the Sector, if not the world in cutting edge research. It's a prestigious place, in case you haven't noticed, EVERYONE wants to get in whether they know about Superhumans or not.
B. The spy course isn't to spy on the Superhuman research, perhaps it's because that's all our Dad ever does, stick his nose where it doesn't belong. And we know Blackmailing the Dean was kind of just for shits and giggles for his own ego, the Dad even mentions he loves getting information on people to use it against them, and there was no way we were getting in a prestigious college by normal means.
C. The mysterious job is just that, a mysterious job because it's SHADY and probably ILLEGAL. He knows people like his friend Jeff (the investigator you mention) loves to get info on him to use against him. If I were up to no good, telling everyone about it would be the LAST thing I'd do. But he also has flaws, because if he was as smart as you seem to make him out to be; he wouldn't have brought us along to spy on his friemisis (Jeff).
D. Knowing about the Monsters is probably all true, no arguments there, our Mother was indeed probably kiled by said Monster and we got our scars from it, and arrived at the same hospital. (Again though, this is Sector 1, the top of the top, everything about it is shady and has their hand deep in the cookie jar of Superhumans as far as companys or businesses go).
E. Yes Dexter trusts our Dad based on the conversation, but I don't think it's as cut and dry as that. The MC mentions a strong grip, most strong grips can psychologically be placed as establishing dominance, i think the last sentence to the MC is more of a warning rather than a friendly gesture. This IS one of if not the most powerful man, you think he'd stupe so low as to pretend to trust OUR Dad? (Blackmail is his middle fuckin name for God's sake). But like I said, I think our Dad was an informat for one of the first Monster cases, not some insider mastermind. And as to why he'd share classified information with us, again, this isn't someone you just stab in the back, he knows it, we know it. He's powerful, hell he's not even phased by knowing the fact that his daughter wants to kill him. He doesn't need to hide government information.
F. Lol no, our Dad isn't fucking Zack. In fact, I'd put money on the two being totally unrelated to some extent. It's one of two options in my opinion. 1, Zack is just a super OP Superhuman, and one of the first of his kind and fought something ridiculous, and got injured for it. And our Dad got injufrom trying to defend us and our Mother from the Monster that attacked us. Or 2. it's semi related, and the monster that attacked us and killed our Mother was one of the Numbered, which explains why Zack got his ass kicked, more that's the reason we were selected by 2 of the Numbered, it would also explain our Dad knowing Dexter, because he was kept on the hush hush as an insider (hence the warning I mentioned earlier). And even IF they were the same person (which they aren't), they can't be because you have to be a certain level of fucking stupid, to one of if not your most reliable INJURED Agent, not be in your sight at all times, let alone having to sneak around against a private investigator (Jeff), who seems to know nothing about Superhumans in the first place.
