Actually, yes, in the event of a new Constitutional Convention, I'd absolutely want to get rid of the 3rd Amendment and replace it with a broader right to privacy. It's not urgent, though. As you say, it just doesn't come up. The religion clause of the 1st Amendment is in dire need of a rewrite, although the problem we have today isn't really that the 1st Amendment is hard to understand, it's that many Americans simply don't believe in the principles of freedom of religion or the separation of church and state, so just making the 1st Amendment clearer might not address the issue - it isn't that they don't understand it, it's that they disagree with it.
My impression of the first amendment is that it is working reasonably well in the United States. As in, there are aspects of it that other countries are quite willing to emulate. The common law and the courts are mucking through.