Disclaimer: I can't stand the Hero system, so take what I'm about to say with a pinch of salt.

1. As I recall (it's been about ten years) any sort of attack linked with armour piercing and/or rapid fire is rather potent. Also keep an eye on disadvantages and make sure players earn their points.

1a. A bigger thing to worry about is making sure that all the powers the players have designed actually work as intended. I'm still bitter about my speedster who, it turned out, didn't have the right level of super-senses to cope with his speed - so as soon as he used his powers he'd run into something and die.

2. Not even remotely. An old edition of Champions I have has several examples of how the system breaks if you've got a lot of points to throw around, my favourite being The Landlord: a normal guy who's sunk enough points into his HQ to cover the entire surface of the Earth. Apparently it's not too tricky to pick up six billion loyal followers, either.

3. If you thought D&D had a chasm between optimized and unoptimized characters, Hero opens an interstellar gulf. A well-built character won't be overwhelming - they'll have an area or two of expertise where they're fantastic, but will be average or worse elsewhere - but a poorly built character will have powers that don't do anything, or act in strange ways because you forgot to buy the appropriate extras. See the above-mentioned speedster, or another character I made whose fire blast was incapable of setting things on fire because that was a different kind of attack.

3a. I did play in a Hero game which circumvented this by having the GM build our characters for us. We told him what we wanted and he used his system expertise to avoid the sort of pitfalls I would blithely wander into.