I think that if their where many different 'transmutation trees' it would work a lot better e.g. iron -> gold -> diamond, but not iron -> enderpearls. This would create further balance as you would still have to conduct various activities in your world (enderman farm) but you could still mine and get whatever mining resource out of that mine that you want. But not get a mob drop from a mining resource or vice versa.
If it took this thread for anyone to realize that then something is wrong mentally. That's the whole idea of the ability to edit the modpack. Don't like a mod? Get rid of it or ignore it. For some of the better mods if you don't like something it does disable it via config. On the same token if you think for yourself something is too weak change it via config. You can even add more mods. You don't need to tell anyone why you don't like it; it's irrelevant. Same with if you like it.