Didn't they do that one year when they were running the Champions tournament as well? Solid Snake won. In the following year Samus won.
Let's be honest, you get rid of Cloud, Mario, and Link, and it just comes down to Samus and Snake. The best way to change it up would be to stop arranging the brackets so the same "top 8" makes it every single year. Link, Mario, Cloud, Sephiroth, Samus, Solid Snake, Mega Man, and sometimes Squall. Same final 8 every single year.
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I'm a genius! Geniuses don't NEED medication!