...but independent doubles can work perfectly well. Has anyone ever dived a single with a pony? What is that config if not independent doubles? Sure, they're "lopsided" twins, but many divers (including the OP) look at their twin 80s (or whatever) as a big-ass pony and manage their gas accordingly.
Background: I dive manifolded twins. I *used* to dive independent doubles. I prefer my present setup. My original config didn't kill me (never came close). I experimented with different reg setups. This is what I learned:
Started out with matching Dacor Viper Tecs, with 2nd stages that swivel to breathe up or down. Ran one over each shoulder. Left reg = left tank = left SPG, etc. Easy to keep track of. Gas management has already been discussed.
Several free-flows later (including one at 170 fsw on a wreck) the Dacors were retired. Blame the regs; not the fault of the config. Switched to Scubapro G-250s, both running over right shoulder. Bungee necklaced one, clipped the other. Got used to which was which, practiced switching in zero vis and/or narced, never had a problem. Borrowed a friend's Posieden to see if I wanted to make that my left-hand reg, didn't like it so stayed with the Scubapros.
To the OP: You only have two choices--run both on the right and learn to deal with it, or use a reg that can run from the left and accept that your reg choices will be limited. Good luck!