I'm dropping this in over here (from your linked site...if it weren't late and I didn't have a term paper due before tomorrow morning I'd poke around and check it out), but I think you're off the mark a bit here. I'm not sure I can see any way to fix this part of the game, nor do I think it's a bug or anyone is claiming that D&D combat is realistic. If we wanted a realistic initiative system for the game, everyone would go at once and the people with the best reflexes would get to act first. I'm being silly, but I'm not sure where you're going with this, as you don't offer an alternative to what the game uses now. The current initiative system is really just a way of ordering a really chaotic thing (combat) into something that is fun and fair (in that everyone gets a turn) for the players. For me, at least, this is a good thing.
Best,
Nick