One of my favorite parts of mods like this and buildcraft are how they give practical use to things that would otherwise be totally useless. For example, excess coal and redstone can be used on powering things or producing diamonds here, and cactus can be used to waterproof pipes in buildcraft. We can use plant material to make plantballs and then convert them into biofuel. Worst case scenario, we have a recycler to eliminate things that are still useless and perhaps use the waste to power a mass fabricator to make useful things.
My suggestion here is to give more use to some things that are currently near-useless in the vanilla game. I feel that would add quality to the experience. They can either be used to make things that already exist in industrialcraft, in a different way; or they can be used to make something new, although that's not strictly what I'm suggesting.
For example, dirt and cobblestone, seeds, vegetable produce, gravel, netherrack, all the things that quickly overwhelm our storage that we are currently just tossing out. Why not come up with something they'd be good for? Any ideas are welcome.