The issue you have is with the entire election structure or just the run-off part? Please expand.
The two are linked. A run off ballot requires single member constituencies. Single Transferable Vote systems requires multi-member constitutencies.
The issue I have with run off ballots are that they aren't a form of proportional representation. They're just an artifical device to give an elected figure the illusion of a majority. Who wins in the first round is in no way representive of the popular will.
Say you have 9 candidates, 1 fascist, 1 communist, and 7 moderates. The facist gets 15% of the vote, the communist 15% and all the rest get 10%. Despite the fact that 70% of people hate fascism and communism, they will all have to choose between the two, and the run off ballot will give one or the other over 50% of the vote.
It's a ridiculous system. Far better are systems where you number of your preferences, 1 for your favourite, 2 for your second favourite, etc.
An "Alternative Vote" system does this for a single member constitutency. The votes for the least favourite are reallocated first, until one candidate gets over 50% of the vote. This gives a genuine majority for the genuinely favourite candidate.
A "Single Transferable Vote" system does the same for a multi-member constituency. So say you have a constituency of 700,000 people, there would be 7 seats availble. Votes will be numbered as with Alternative Vote, but instead of 1 being chosen, 7 will be. The result is 'proportional representation' where the different candidates chosen reflect the diversity in views of the people. So if the voters are 3/7ths socialist and 4/7ths liberal, you'll probably get 3 Socialist candidates elected for the area and 4 Liberals elected.