Between the two options you are giving there's a significant difference. The SPD-SL pedals use a larger cleat with a road style bolt pattern. That limits you to road style shoes. They may be more comfortable, especially for longer rides because they spread the pressure out over a larger area and generally have a stiffer sole. I find them easy to clip in with.

The Eggbeaters use a mountain bolt pattern, which is still usable with many road style shoes but opens up the possibility of using a mountain bike style shoe. They are usually much easier to walk around in.

I ride SPD-SLs, my wife rides Eggbeaters. Both are good systems, but neither of us has tried the other system so i can't make a direct comparison. The other options may be good for you too, I was just working within the confines of what you were already considering.