Endermen cannot teleport into blocks that are beneath water or lava. If you place your spawner in a room that is directly above the sea, where there are no blocks in a 32x32 area that they can teleport into, you can then cover the entire floor of the kill room with water leading into transposers that collect the enderpearls and lead them into storage. The reason for the 32x32 area, is that they can teleport outside of solid blocks, but only to a certain range, which is 32x32. With this setup, what should happen, is that the Endermen fall into water, start taking damage, but can't teleport anywhere else, because there isn't anywhere else to teleport to that they can access, so they'll just stand still until the water kills them, and the items are collected by the transposers. Be sure to also cover the roof of your building with water as well, so they can't teleport into the roof of your building.
The best setup would be a 11x11x9 room, with the spawner positioned smack in the middle of the interior 9x9x7 space, so in the middle block 3 up from the ground, and 4 away from every wall. This gives you maximum spawning coverage for the spawner, which will be able to spawn the maximum amount of endermen possible. You set up water source blocks all around 2 sides of the room, leading into the central line, which will be covered from the water streams using signs (because water can't traverse signs, but items still can), and finally, that final line which is dry, you cover with transposers. You can make the floor of the room out of ice so that the items traverse more quickly to the transposers, and so cause less lag. You'll also want to cover up the transposers with water, putting a water source block on either side of the line, so that the water flows to the center. This won't prevent the items from getting sucked up into the transposers, but will prevent the endermen from teleporting to the transposers and being safe from the water there.
This is more efficient and reliable than the fall trap. If you don't have an ocean nearby, you can also set up a Mystcraft age using either the Ocean biome, or a Void age, and this will also prevent the endermen from being able to teleport away. I'd most certainly recommend the Void age, since the endermen may still be able to teleport to BELOW your trap in an ocean biome if there are any empty spaces available in the Y axis, so either make sure that that's not the case, or set the trap high up in the sky, so they can't teleport vertically out of harm.
Test this setup in a creative test world. I'm thinking you'll rather like it
You'll know if it's working if they don't move at all after being damaged by water.
EDIT: You don't actually need the stuff with the signs and water streams if you just make your floor out of transposers and just put a layer of water on top of it. All items will still get sucked by the transposers, and it will actually cause a bit less lag that way.