incoming wall-o-opinions:
Ore & World-Gen:
In my opinion, a mod like yours would be more of a world-gen replacement, than an addition...at least for the general metals (copper, alluminum, tin, silver, etc...). Metallurgy is all about mining and metal-work...be it making tools/weapons, coins, etc... I think your best bet here is to make your world-gen so robust that the best option for most users is to just disable other mod's world gen in favor of yours. Give people the options to set the size of the nodes, the height that nodes can spawn, options to specify which biomes each ore can spawn in, etc... In your config, set the defaults for how you envision the world-gen to be. From there, the only thing that is needed is to provide a basic tutorial on how to disable other redundant world-gen (and possibly adjustments to your config to account for the additional quantity needed for the other mod(s)).
From my point of view, the biggest decision to make here is how much compatability you are willing to try and build into the new version of Metallurgy. With upcoming mods like Electrodynamics (
http://www.electrodynamicsmod.com/blocks/4576161533) adding ore that will provide multiple kinds of metal dusts when processed, you run into issues with different ore providing the same kind of metal when processed.
Metal (processed dusts/ingots) & crafting
This seems like the point where balance concerns come in. Metallurgy's way of making one type of ingot might be harder/easier than another mod's method. I don't see any way around this short of collaborating with all other mod authors and coming to a compromise. Ultimately it's going to be up to the user to decide what is balanced. If something seems too easy, there's nothing (besides sweet-sweet temptation) making players use the easy method. I think the only thing that will alleviate this problem is something like a config setting for disabling crafting recipes, so moderators can disallow certain ways of obtaining items/materials on their servers. Adding these kinds of configs to Metallurgy will help solve the problem, but I don't feel there is anything that any ONE mod can do to fix a problem across the entire modding community.
Machines
As far as machines, I'd like to see a method that has never been used before. The reason it may have never been used is because it's not possible, but hopefully not...hopefully it just hasn't been considered, but I doubt that.....Anyway...follow me here. When you make something like a rock-crusher out of basic things like stone slabs, that slam together & crush anything in-between them, it's 1) Not very efficient 2) rough on the material & machinery 3) not something that you would WANT to upgrade to a new material even if you could. Once you got to the next tier, you'd want to innovate & improve the process...you wouldn't want to just make 2 iron slabs that would replace the old stone ones you were using to crush you ore, previously...you'd want to build iron grinding cylinders that when turned together would crush anything put into them into a more refined material than was possible by just bashing them with stones. On the same note, you wouldn't include your old stone crusher in the recipe for your new iron grinder, either...it doesn't make sense. Therefor, as you move through the tiers of technology, the previous technology becomes obsolete. There is no longer any reason to make a stone crusher, just to upgrade it to an iron one...that's progress. "But, Zahfelade!!" you say. "Now I have a useless crusher sitting around my base taking up space." So, why not give your machinery a durability cost. Let them burn themselves out after a certain number of uses. Once they come to the end of their life-cycle, they break, returning a bit of the material used to craft them. This gives you one more use for the different tiers of metal & machinery. Once you work your way up to the highest tier, that machine is unbreakable. Viola! No more useless machine clutter, no more nonsensical upgrade/machine tier system, no more set-it-and-forget-it ore processing systems (until you reach the highest tier), plus you get another reason to go find better & brighter metals.
So, in short: Don't do a straight "better-version-of-the-same-machine" upgrade system, and don't just do one machine that never changes outside of the GUI. Come up with new machines for different tiers, or come up with a multi-block machine where the "upgrade" piece is one of the blocks that are used to the structure & ultimately change the look/feel of the finished product.
Again, these are just my opinions...but these are some of the reasons that I have opted for not including Metallurgy in my worlds in the past. Hope this helps.