Ah, well, no you can't get around that limit.
WiiRD, the software used on the PC side to see the memory, is limited by this as well. So, unfortunately, there isn't a way to increase or change the limit. The limit is based on the Wii's RAM, the majority of it being taken up by what it loads in the game, with what very little is leftover is what is used for the codes (the 256 limit).
The AR (for GCN) also had this type of limit I noticed but, I didn't know how much, all I knew was that I couldn't have EVERY single code on that I wanted, I was only allotted a certain amount of Super character codes and infinite jumping and etc. For the Wii, it's kind of the same, except even lesser so because of how long some codes are now.
Don't know if there'd be any way around this to make your idea work. The best thing to do would be to buff the characters that'd need to be buffed and nerf Meta Knight and a few of the Top Tier to make it a little more even footing. But, even then, that's asking for other characters to be buffed/nerfed... meh.
I'd be interested in seeing this work out somehow though. Hitstun would be the highest of priority though, unfortunately, Phantom Wings seems to be incredibly busy and very reluctant to making any codes that would make Brawl seem more like Melee.
tl;dr - Can't change the limit in any way because of the Wii's RAM.