So, I've had this addon installed on my server for a few days, and my first reaction is that it's conceptually amazing. I love what the Industrial Centrifuge does, as well as the Fusion Reactor. Except, I've never gotten the chance to use the Fusion Reactor. Or the Lightning Rod. Or the Matter Fabricator, for that matter. And that leads to my major issue with the addon: You require iridium to get iridium. Every single possible pathway into the addon (UU-Matter generation to craft iridium, using the Fusion Reactor to create iridium, or using the Lightning Rod to generate enough power to strip-mine quickly enough to find iridium) is cut off until iridium is initially obtained, the starting amount being 5 plates, meaning 10 ores (20 if you neglect to use one of the grinders.) need to be found. If a 64x64 quarry finds 3 ores on average, you'd need to run four such quarries from start to finish, something that could take days unless you had them all running simultaneously.
This is terrible design for a few reasons.
1. You act under the assumption that the player has Buildcraft. While it's a reasonable assumption, your only prerequisites for using the addon are IndustrialCraft, and by extension, Forge. Anything that can't be found in IndustrialCraft needs to independently exist in your mod.
2. The steep requirement for iridium makes it one of the most difficult materials to obtain in any mod I've ever used. You've not only made it a key ingredient in most of your recipes, but also even harder to get. Something so fundamental should be relatively easy to obtain (See: Sticky resin) while the more powerful devices should require the rare materials. (This is why regular batteries aren't made of diamonds.)
3. That leads to my next point. All of your machines exist on the same level. I see no reason to pick the Fusion Reactor over the Lightning Rod, or vice-versa. I guess my decision would really be based on whether I have more Deuterium/Tritium/Helium cells, or if I have a consistent way of creating lightning. The idea of a Lightning Rod is great, but the effort invested into getting one up and running simply isn't worth it to me, who hasn't seen it in action. An LV, MV, and HV version would go far to encourage me to investiage the technology, as would simpler Fusion Reactors that simply fuse hydrogen into molecular hydrogen, or maybe helium.
4. Conversely, your Industrial Centrifuge is incredibly easy to obtain. From a design perspective, it's clearly the entry-block into the mod, just as the iron furnace is the entry block to IndustrialCraft. However, all it does it consume my cells and junk materials, and after a really long time, it pops out some other junk materials, and new, strange materials that I have no idea how to use. The only thing I'm really getting out of it are new sources of fuel, but honestly the time they take to make makes them feel more like a novelty, and the fact that there are future uses for them makes me hesitant to use what I have.
5. I've seen somewhat similar complaints to these before, and you wave away the big one, the fact that iridium is so rare, by saying that the rarity is configurable. However, this is a poor argument. Whenever Game Informer, for example, receives a game to review, they play the game on the normal/medium difficulty. The reason for this is that this is the default difficulty, just like the values you set in your config are the default settings. This is the way that you choose to present your mod to the community. Changing it for myself is, to me, cheating. It's no different than me adding items to my inventory via NEI.
So, my suggestions:
1. Make iridium, not necessarily more common in spawning, but more obtainable. Add different ways to get it. Maybe have a dust that centrifuges into a small amount of iridium dust, a stack of which is compressed to become a single iridium ore. Spending days managing quarries is simply not acceptable, and it becomes all-or-nothing luck.
2. Make iridium more visually distinct than the myriad of other light gray ores, and make sure that if it spawns in a chunk, it's visible if possible.
3. Allow your Industrial Centrifuge to be a gateway to additional parts of a mod. In the Matter Fabricator's recipe, the only thing the Industrial Centrifuge does for me is get chrome and aluminum ingots. Meanwhile I have a chest filled with two dozen different by-products that have no use until I get highly advanced machines.
4. Break your machines up into multiple tiers. Let the lower tiers not require any iridium.
5. Generally make your mod less soul-crushing. The 'ooh, I want to make that' moment was ripped out of me when I checked what I needed to make a machine. And then checked what I needed to make those parts. And so on. Crafting complexity is great, but those intermediate parts better do something, or they're just an excuse to use up tons of expensive materials.
I need to emphasize one important fact: I love the idea of your mod. I'd probably love the mod too if I could utilize it. I know I must be coming off as abrasive and extremely critical, but it's, as cheesy as it sounds, only because I know that there's so much potential here, and I know you can achieve that potential.