I've argued before that if we are going to have a notwithstanding clause with continued popular legitimacy, it needs to import a super-majority requirement, so that overriding a Charter decision isn't just routine.
Commenter BKN asks whether there is not a "constitutional convention" against the use of the notwithstanding clause. He also suggests that the Court is too smart politically to ever strike down legislation so popular that a super-majority could be summoned against it.
One response on the political savviness of the courts is that the Court has struck down a number of laws which Parliament simply reenacted, sometimes without much of an attempt to address the court decision, and the court has usually just accepted this. One example that comes to mind is the "drunkenness" defence, struck down in Daviault: see Kent Roach's article on this phenomenon here. As long as courts react this way, then the override becomes unnecessary.
Has a political convention emerged against the use of the notwithstanding clause, no matter the circumstances? I tend to think the last federal election disposes of that idea. Martin got no real bump from proposing to do away with the notwithstanding clause for the federal government. Harper defended it effectively.
The genuine difficulty is that the notwithstanding clause can only coexist with judicial review if its use is at least somewhat exceptional. I think the best way to underline that it is exceptional, while legitimizing its more frequent use, is to add a super-majority requirement.