I feel that is you have a large open server, it is wise to turn off some (or all) or EE. For personal servers or smaller servers I think that it is fine because if it is a small amount of people they wont grief or use duping bugs, or at least that is what I have seen. When saying it is OP that is only true at the end game. Starting out EE is somewhat difficult because you need four diamonds, a decent amount. As for"not playing nice with other mods" I think that doesn't make sense. Red power and buildcraft both have pipes and industrial craft and buildcraft have miners. When putting any "big" mods together there will be overlap that makes things obsolete. Then for getting every item from a transmutaion table, well first you need the item. That might not seem like much but finding some blocks/items is difficult.