Quite simply... they can't. Those enemies have to be there, and have to respawn quickly so that other players can complete quests and generally have the same experience as you. This game has a "shared world"... the idea is to have that world be as similar for each player as possible. It's not Halo, where they can dictate exactly how you're going to enter each area every time, and they can't predict what other players are going to do when it comes to affecting your experience. They've handled this far better than any MMO I've seen/played, though. Most of them just have groups of 3-5 enemies, all scattered all over the area randomly, and they just materialize out of thin air a short time after you kill them. At least Bungie took care to make enemies spawn a little more organically, and appear in various numbers... so as not to look as though they just copy-pasted a bunch of generic enemy groups all over the place for players to farm.

Well area's such as the downed guardian ship and other story areas would not be changed. But the bland respawning enemies would be replaced by unique patrols that follow a set path through the map.

It's a nice thought, but I don't think it's going to happen. Like I said, they could have handled it just like every other MMO and just had enemies standing in completely static locations, who materialize out of thin air shortly after being killed. Boss enemies just standing right there in the world, waiting to be engaged by whoever comes along... Instead, they have spawn rooms where enemies only spawn when nobody is nearby, or they'll spawn from drop ships that cover them as they exit the craft... boss enemies spawn the same way. It's handled well enough, as far as I'm concerned. No matter how many times it happened, I always got a little excited when the sky turned black, and "Defeat the Fallen Walker" scrolled across my screen...