Fridge Logic: If Zodon uses his mechanical arms to manipulate everything (as we have seen him do every time on screen), then how does a DNA scan work to keep him out of the school's systems?
No DNA, no worky. Duh.
*points at Doctor Positron*
He gets a special dispensation, as the system was designed with him in mind. And maybe that helps explain how Zodon was able to use a calculator and a Speak-N-Spell to overcome the locks that first time...
Rainmaker kids crimefighting
The kid who can turn stuff into food. The ground under a criminal is stuff. Soup is food. It would be a perfectly effective power for fighting crime. It's certainly better used for things other than crime-fighting, but what isn't? So why is he in the rainmaker program?
Because while yes, in theory you could use your power to sort-of fight off normal criminals, imagine what happens when you're up against a super-powered criminal. 'Oh look you made the ground beneath me soup, woe is me-oh, wait, I HAVE EYE BEAMS! *ZAP*'
Also, he specifically says that he can't change what it looks like, just how edible it is and how it tastes and suchlike. He can make a brick taste like chicken soup, but he can't quite make it look like it just yet.
It doesn't matter what it looks like. It matters what the consistency is. He can make a brick edible, which means he's messing with the consistency.
The distraction lasts long enough to make a big difference for the fight. Much larger than the advantage eye beams give over conventional firearms. In addition, it can be used from behind cover, and following it with turning the soup into hard candy would effectively end the fight.
So far, it appears he has to touch the thing to make it work. There may be some limitation in how his powers work that keep him from being able to do this productively.
Has he ever not been touching the ground? As long as it's not nearly as deep under himself, it should work fine.
The whole Rainmaker arc demonstrates that all of the Rainmaker kids have powers that could be used for crime-fighting. Presumably they get put in the program if they have abilities that are clearly much better suited for something else, or if they or their parents simply prefer a non-violent career path.
All of them have powers that are much better suited for something else. The vast majority of things are not fighting crime, so it would be rare for that to be the ideal use of a given power. The rainmaker group isn't even particularly good. A genius inventor could do more to feed the world than someone who has to be present to make food.
Mister Extraordinary and FISS
Is Mister Extraordinary counted on the F.I.S.S. list? He never used his flight powers in front of anyone other than his family, resulting in them being pretty much unknown. If he's not on the list, then the entire list needs to be rewritten, as he was the first documented meta-human, making him the first F.I.S.S.
Or he's number zero.
There's also probably quite a few metahumans they don't know about. The list isn't intended to be perfect.
Lack of Secret Service Protection
If Principal Cranston used to be President, where's his Secret Service detail?
For that matter, where is any acknowledgment of his former presidency anywhere outside of flashbacks? Was the knowledge magically/psychically retconned from everyone's memory?
No, it was hinted at quite early on, far before it was revealed. Issue #6, I think, the first with American Eagle and Patriot Act.
Also, most of the comic is from the perspective of the kids. Not many kids in elementary school are going to be that conscious of former presidents, especially ones that were serving when they were infants or not even born yet (depending on precisely how long ago Cranston was in the Oval Office). For a lot of the kids, not realizing half their teachers are former members of a popular superteam is more unlikely.
You can decline Secret Service protection as long as you are not the current (Vice) President or the (Vice) President elect. Presumably Cranston waived Secret Service protection to help put that part of his life behind him.
Considering his flashback implies he was unofficially impeached and removed from office due to violating a constitutional amendment banning metahumans from office, it's likely the lack of Secret Service and acknowledgement is due to having become an Un-Person in American politics.
Obstruction during an alien invasion
Is that Obstructive Bureaucrat Ms. Riley really so stupid/insane that she's willing to put a meeting over an alien invasion with multiple students and faculty in direct danger? There's a time and a place for these things, and that's not it.
Her point was that she needed Cranston to help deal with Praetorian Academy, and he was not actually needed for the invasion until he had to sign that permission slip. He's not a general. In her opinion, he would have been more useful in his capacity as principal, helping her figure out what to do about the Obviously Evil rival school that was about to siphon their kids away.