Certainly I'd keep the EOB if you can get it working - not because it's preferable, but because it is in place and, in a manner of speaking, it "works".
But, its operating characteristics are fairly awful. It always makes a loco start as if it were pulling a 200-car train, even if running light (no train), which is simply wrong, and it buffers throttle commands - it does not answer the helm in real time, so that if you are trying to get it to act at least a bit realistically (not acting like a snail), all of a sudden the engine is doing 100 mph from your earlier throttle inputs.
So, smoke 'em if you've got 'em, but I have 2 or 3 with EOB, and I leave it turned off (as in my Atlas RS-3 - try switching with this unresponsive setup!). Acts better; the 3rd Rail gearing is probably pretty good, anyway.
All this is while running TMCC, in my case.
