I'd like to re-submit Metallurgy for consideration now that it's about to go 1.5-ready. Metallurgy is not unbalanced and can be a real boon to modpack maintainers because it can take over ALL ore generation and have that handled in a consistent way, sort of like what TE is doing right now but on a grander scale. It also allows for piecewise inclusion of metals for the different packs, which is great. The fantasy metals pack might be appropriate for Magic World, but maybe not for a more industrial pack. It also significantly opens up opportunities for mining in the nether and End, which currently only gregtech really does.
It also adds a variety of useful alloys, and there are several mods out there that help to integrate metallurgy with other packs to make these alloys even more useful. The way Iron gets dispersed means that you actually need to alloy at least to bronze to succeed in the early game, which seems good to me.
Finally, its machines are actually pretty balanced in the current metagame when you consider Thermal Expansion. Any machine that uses the furnace model of fuel (one unit is ignited and runs out and does all the work it can) will always be at a disadvantage compared to the electrical/mechanical machines that can turn coal into smaller units of power for more efficiency, and the inclusion of something nicer than IronChests is great as well (Iron Chests is... really good and easy; Metallurgy Chests are somewhat more challenging). Considering that AE also gives a very early ore doubler (using player time instead of fuel), there really aren't any balance concerns at all for a properly configured mod.
And note that M2's default config actually makes mining for many things more difficult because you can't rely on specific Y-levels to yield specific things!