There's no such thing as a perfect voting system due to Arrow's impossibility theorem, so you're just trading off disadvantages. The main problem with a standard top-two runoff (which is pretty much equivalent to an open primary) is vote splitting between candidates of the same party. The advantages are that it's easy to understand, easy to explain to people, easy to implement without major changes to voting machines, and is already in use by several states. This makes it much more likely to be switched to in practice. Perfect? No, but neither is instant runoff voting.
Fun tidbit: I have a book (Game Theory, third edition, by Guillermo Owen) which provides an example of an electorate where six different voting systems, including ranked choice, each result in a different candidate being elected! The theory of voting systems is really weird. Edit: I can't find the example in that book, I may be misremembering which book it's from.