Re: the idea of a -Rep penalty for attacking lower-level people: it's unnecessary. Wasting your time fighting for 0xp is just as bad as sitting in Spirit World, only you risk actually going to Spirit World for doing so.
Also, I think the 'lower level' limit shouldn't be a cutoff, but a diminishing return. As in, if you fight someone within 3 levels of you, it's considered 'even', but if you fight someone 4 levels lower, you get -1 discard/salvage; 5 levels lower, it's -2 discard/salvage, and so on. Needless to say, if you win against someone 4 levels higher, you get +1 discard/salvage, and so on. That way, there's a bit of a larger range of attack (which is a good thing), and you make getting attacked by a higher-level player into an opportunity for the victim as well.
In terms of resetting characters, I'm liking the idea of a few non-elementally-aligned "Elite" skill trees. You gain 1 Elite skill for reaching Character Level 31 (or whatever), and Elite skills carry over between characters. They don't even have to be all that unique or special; something like "You may always use 2 extra upgraded cards in a fight." or "You gain access to a single Mark of your choice." is just fine. The point isn't that Elite skills are appropriate for CL31, it's that they're small boosts for characters of any level but aren't overpowering at CL1.
I'd create say, 3 trees just to give Elite players the illusion of choice, but make all of the bonuses small ones. The satisfaction of being able to carry something over and call yourself Elite is the real prize.