The portal gun mods. No question. You can find them in dungeon chests, and they're cheesy: lets you move any block AND acts like silk touch when you place a block in a door or over a torch. Imagine being able to find a jackhammer in dungeon chests, along with an infinite power source for it! Portal Gun is really just a feature exercise, like any other cute mod that adds a fun thing purely FOR that fun thing, with no consideration for balance. Its main purpose is made redundant with Mystcraft anyway. If you really want it, use the Direwolf pack, I say. It also sort of bothers me that it directly apes Portal with no changes. Mystcraft is inspired by Myst, but doesn't slavishly reproduce it. It's like if FTB were to have a Mario mod. Even if it's cool, it feels...suspect, copyright-wise.
Getting rid of RP is tempting, especially since you know RL work is going to be a permanent problem for Elo. That said, I don't think I could ever give up RP terrain gen. Or the actual logic, since that's sort of the point of RP and it's lovely. In fact, if everything else in her mod - even frames - got replicated by some other mod, it wouldn't bother me. But if someone made a mod to replace RP logic, I would be really sad.
I don't think I'd take out EE3, but I'd nerf the HELL out of the Minium stone. It needs its list of transmutations cut down (leave the smelting shortcut for the philosopher's stone), and should have the durability of gold items.