1: Inventory size is a game design question about how mobile the author wants you to be, and with most things being stationary, you obviously shouldn't be too mobile. Whether or not the player likes that is a different question. For everything else there is a teleporter and the ender chest, although those are not helping on a nomad play-style.
2: Again, game design problem: The Quantum Suit makes you mostly invincible, the only drawback is that your electric items can no longer be recharged by your pack. If that pack would be integrated into the quantum suit, you would be invincible and have no drawbacks at all. Imo the whole quantum suit concept is too op to be reasonable even though you need massive amounts of EU to produce it. Once you have it, you basically won the game.
3: There are already some compatibility parts in IC² to work with RP, BC and other mods, but the more you add the more complex the whole thing becomes. It is already a nightmare to keep up with Forge/Minecraft development as you basically need to rewrite half of the code every 3 month. Add a few other mods, and you can hire a complete team just to keep the addon compatible. And not every other mod author is that cooperative, when I remember the result from the talk to Eloraam. So for a single hobby author leaving the task to make mods compatible to other people is a reasonable thing to do.
4: I would love to see some use for those dead parts instead of just removing them. Some things can easily be turned into viable options easily, e.g. I wrote a quick 3-line addon to change the recipe for dynamite and voilà they are a reasonable early-game alternative to mining. Similar things could be done to bio-fuel, for example making it a non-metallic Tier-0 set (compost reactor ;)), or giving it extra abilities that makes them an option compared to the usual way. This however requires time and thinking, and from my perspective it looks like the IC-team does not spend the major part of their day on advancing the mod.
5: Absolutely agree. You can't just build a nuclear reactor on a public server as griefers just need to flip out some components and boom there go your days of working. But just adding a pass-code to the reactor would cause people to just wrench it instead. There should be a way to secure reinforced doors, so they only open given a certain pass-code, then you can spend the resources and build a secure room for your reactor. This still would not stop all griefers, but building a laser before you can break in somewhere takes at least enough time to stop most server hoppers from griefing you.
The nuclear bomb can be deactivated via config, and I strongly suggest to do that as a server admin. I would even go that far and deactivate it by default, as the bomb actually servers no other purpose than to create a huge explosion.
). Please note that I didn't research these bugs, so I can't tell you whether they were just random or happen all the time.