I do seem to recall that we've had propositions in California that were conditionally tied to each other -- Prop. N specifically says it takes effect only if Prop. N - 1 fails, or something like that -- so I think this kind of problem can be addressed, if the initiative drafters do their work well.

A bigger problem, in my opinion, is that a bare majority is sufficient to amend the state Constitution. I think at least a 60% supermajority should be required.