The question shouldn't be how iconic is Master Chief in regards to other third-party characters - he's a legend among legends, answer is already self-evident. In terms of stature, he wouldn't be out of place standing next to Sonic and Pac-Man.
Rather, the question should be whether or not Master Chief (or anybody like him) having no history on Nintendo consoles (cancelled games don't count) can be considered a strike or not. Of all the "fan-rules" (or whatever you like to call them), this has yet to be "broken".
Some say the "rule" exists and is firmly grounded in reason, and others say it's made-up conjuncture and will be "broken" like any other "rule". Regardless, that's ultimately the one obstacle that should be overcome by anyone arguing Master Chief would be a reasonable Smash fighter.