1. The powers of the federal government are limited to only what is positively given to it. Hence, the second amendment is largely unnecessary (which is why it wasn't part of the original Constitution - not because the Founders didn't think that people had a right to arm themselves). So the feds may not even regulate nuclear weapons ownership, because they were never given that power to begin with.
2. Your arguments regarding the discriminatory capabilities of various weapons make plenty of sense, but they have little or no bearing on what the second amendment says (see my #14). If we want the law to make such distinctions (which weren't a concern in 1791), then we'd have to pass another constitutional amendment.
3. The fact that the feds don't have the direct power to regulate nuclear weapons doesn't mean that they can't be regulated: the states still retain that power. Some might object that the "privileges and immunities" clause of the 14th amendment extends the protections of the Bill of Rights against state governments. I realize that the federal courts have ruled that it does, as they're much more comfortable with restricting the states than restricting the feds, but it should be noted that they didn't start ruling that way until several decades after the amendment was passed. Privileges and immunities don't seem to be the same thing as rights.
All of our rights are bracketed by the existence of our fellow-citizens rights. (Free speech and yelling fire in a crowded theater, etc etc). This should be self-evident. To argue against that is to argue you have superior rights to everyone else.