Boris Johnson controversially scheduled a prorogation of 34 days recently, which means that the UK Parliament won't be able to pass new laws at a critical time when the UK is about to leave the European Union. But could the MPs get around the prorogation by passing a new law? Given that the Parliament is supreme in the UK, what could possibly stop them from completely rewriting the rules at will?
Passing laws takes time, which is in extremely short supply.
The final deadline is the 31st of October. The real deadline, at least at the moment, is the 17th of October (the final EU summit before Brexit day, and the last "regular" opportunity to ask for an extension). Parliament will be prorogued from some time next week (of the 9th of September) and return on the 14th of October. When they return, all pending legislation from the previous session is considered dead, and must be reintroduced from scratch. This means that each law must be passed entirely before or after the prorogation, and the process cannot be split across it.
For a bill to become law, it must, at an absolute minimum, get three readings in the Commons, three readings in the Lords, and then go to the monarch for royal assent. It will be extremely difficult to squeeze all of that into such a short window of time. Therefore, the MPs trying to prevent a no-deal outcome are focusing on completing the most critical legislation (to require the PM to request an extension at the aforementioned summit). A large-scale restructuring of the royal prerogative is simply too ambitious for the available time.
Prorogation is a royal prerogative.
Parliament can modify royal prerogatives, or appropriate them, but to do so it requires the Queen's consent, which in practice means the consent of the government. (See here for an explanation of Queen's consent in the context of the September 2019 anti-no-deal bill).