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What you are asking for is balancing against other mods, which really isn't his responsibility. While it is possible to balance against other mods this falls more under your responsibility then the mods. I will try to look at your points and pick out what can already be done with the mods
1.While you can't do anything about upgrading to the advanced solar panel being too cheap, you can use Greg Tech's recipe for the solar panel itself, which is much more expensive then the original. If you feel that getting the materials for Greg Tech's solar panel is still too cheap (aka steel via RailCraft blast furnace.) then only use Greg Tech's industrial blast furnace, which is much more expensive. You can also use the config for this mod and change the outputs to what you feel is right. If you feel the advanced solar panel is not costly enough for 8 eu a day, then tone it down. make it output 4 eu a day, or 2. whatever you think is right. Its in the config.
2. If you feel that nuclear power is being shadowed by solar panels, then up the efficiency in the IC2 config. If nuclear reactors generate a lot of power, compared to its cost, people will use it.
3. This one has a few so let me get through them one at a time.
Teleporting lava form the nether. I believe this is the RailCraft + MystCraft crystal portals? You can disable the crystals symbol in the config, or the Receptacle. Both will make this impossible.
Dense Ores. Can be disabled in the config.
Forestry farms as a whole are pretty self sustaining. I can't really think of a way around this except to disable all the farms via the config.
Iridium generation. You can either stop the generation via the Greg Tech config, or increase its rarity to your liking.
4. You can reduce the higher tier solar panels to be less effective, or increase the effectiveness of the nuclear reactor.
5. You can turn the night generation for all the advanced solar panels off. Making them generate 0 eu all night. This is all I can really think of for making wind/watermills useful.
I hope I am not coming off as aggressive, or snooty, or anything negative. I did not mean to be. I am just trying to say the mods give you a lot of power in making whatever experience you want.
Thank you for Reading.