The screen-locking thing for co-op seems a bit strange, considering the relatively low field of view due to the 3DS screen.
I've seen a Mario hack that splits the screen in real time horizontally, vertically, and even both at the same time if the situation presents itself. You'd be surprised how well it actually works. It does jar you from time to time, but overall, it's a pretty unique way of handling two players on the screen simultaneously.
I believe co-op in DKCR automatically transports you back to whatever character is on the screen, in most situations, if you're off-screen long enough, and not about to come in contact with any type of hazard. (There's a set time limit until this happens).
The best solution is... you have two players, two 3DS', their own separate screens, obviously: just let the players roam about, and give some possible indication as to where the other character is in relation to your screen. Cuz it'd sure suck to be gaining momentum for a big jump only to be halted in mid-air by the slower character; on the flipside, if it gives screen priority to the leading character, it'd suck to be the trailing character getting dragged by the leading character.