1) I want to play a character with the pragmatic thinking of The Punisher but with the powerset of The Flash or Superman. Would you disallow this because it breaks genre to have such a powerful character be a pragmatic?
If I let that characetr into the game, we would stop playing the Super Hero Genre. Then again, I could unleash all the painful realism (such as scared government agencies with all that super sciencing hiding there or other hero groups - painfully powerful who want to stop you before you do things that will get them all incarcerated/ banned or force them to take over the world.). Again, we moved out of comic styled super hero games and moved into a game with powers. (Super Agents/ Meta Agents.)
You would say "why not?". I would ask you would you let a Camalot Paladin into your all thieves game? Would you let a guy in a bozo the clown suit (and must wear it all the time) into your espionage team? Would you let a guy in a bathrobe and pointy hat who claims to be a wizard (and is) into your science fiction mercenary campaign (okay you might). Now if we were running a different kind of game, sure the character would work. If we are running a comic book styled game... no.
2) Now this one is open. It is not just genre involved in that, so I can't correctly address that one. Novel use of powers (and use of the rules mechanics - which as we went through - usually support the reality bending super speed of comics) is just another way to play.
Supers games tend to be about "powers you have" and "powers the GM approved". Going beyond that because you logically should be able to, you have basically decided to ignore character creation and game rules. Minor things, okay. Major things, it would be like a fantasy character casting some spell (you would then say, you can't not on your sheet... he would say it is logical that I could). If you want to use reality to do certain things, that is okay. Your GM might let you. Then you will discover that reality cuts both ways as that piece of road debris rips through your thigh like a large cal bullet.
Lack of genre application is usually dealt with by XP reduction. Again, using another genre as an example - the Pendragon example - If you ducked the knight at the bridge, you are not playing in the spirit of the game. Sure you might be playing smart, but you are not playing Pendragon.
Genre compliance is a spirit of game compliance. One of the reasons many people have unsatisfying Supers Games experiences is because either the GM or the Players "don't get it". (Don't believe me, look at the number of people in the favorite/ least favorite thread). Sure they are playing the "playing smart, and if I had powers we would do it this way", but that won't be a comic game. It will be a game with powers. Playing that ways works a false expectation. You expect a fun comic game, what you end up with a game with powers, a munchkin run in many ways. That is why most people dislike supers gamings. It takes a lot of work to do it right.
Back to topic, Repeated non compliance, ends up like this... "Okay, you solved the problem. Well that was a fun 20 minutes. Time to go home. See you next week. Oh and since it wasn't that much of a challange, 1 EP for showing up (instead of your normal 3). "
Many of the lack of genre related solutions will come from ingame consequences.
**Okay, you stopped the criminal by causing every pane of glass to fall out of every building on the block, here is a law suit for 2 million dollars for the glass and some endangerment suits.
**Okay, you killed him. I need to arrest you now so we can book you and set your trial date.
***Oh you decide to flaunt your vigilante status and ignore public outcry from above, well try doing "heroics" without popular support and now the law will be after you
**Here comes the traditional solutions to "perceived rogue supers", Other Supers teams. Are your friends going to back you up and go to jail or bail? There are other teams out there.
2) A - The current Flash, not that smart... so we don't have an issue. However, I get your point. So are you mentioning this as genre breaking as actions or genre breaking as applying real physics to get a cool effect (and getting effects you didn't buy in game)? Two very different things.
You signed on for a supers game. You should strive to solve the issues along genre lines (See the Pendragon Knight example) Sure, you might slide a bit from time to time, it should be okay (unless your GM is more of a #$@# than me). If you don't want to play it, then fine, Just why would you be there.
The rubber physics... that gets messy. Once the physics switch gets thrown, it all goes south. It becomes harder for the GM to play (even if he is a physics major, like I was) and harder for the PCs to play. Powers break/ bend a lot of physics rules.
To address one last thing...
For me at least, this would totally suck to play.
Hence why you should not be playing. And that is okay. You are not a supers player. The bit about Supers Play is trying to show how good you are by how well you can work in their rules. Just like a Noir game is about showing how well you can be the cynical protagonist, or a Pendragon game about being a honorable knight. Any of these may not be their cup of team. And that is why we have so many different kinds of games.