Yea, the Transmutation Table was awesome, but one has to admit that having one flat value sort of breaks a few mods balanced around the concept of a few different kinds of "currency," (namely the specific metals, along with growable resources, et cetera et cetera.) GT before it went psycho was probably a good example of this. TC3's system of using multiple Essences is a good example of an alternative transmutation system, though TC3 doesn't properly allow many transmutations. This is made worse by the fact that shortly after acquiring a DM Hammer, you've pretty much got access to ungodly amounts of just about everything in the ground, so just not having EMC values won't help, you also have to not be too dependent on ores.
Another thing is it makes other mods' infrastructure totally obsolete. Once you have a Collector and possibly a mob farm, which mind you, take a little while but aren't that hard to get, there's no need to set up a Macerator or Recycler. The Compressor's mostly just for progression, the Extractor doesn't offer anything that EE2 can't trump right off the bat, the Massfab's already been replaced. That's most of IC2 already knocked out. Most other mods ran into similar problems. BC and RP2 are excluded from this, given that they're more centred on things other than item processing (BC's for allowing it instead of actually doing it and RP2 is just stuff.)
In short, yes, EE2 was quite well-balanced against itself (which was basically Creative after 5 hours, but meh,) but when you start adding other mods into the mix, it towers over them and dominates the game.
Back to your statement about EE3, I do agree that the way it's going right now isn't the right way, but it's still very much a WIP. Most of EE2's features will make a return in some way or another, though I think Pahimar's planning to make it more balanced around other mods' standards.