Of the many problems, the biggest is that - if I've understood it correctly - it ignores any and all events after the first chance given in an innings. Why, for what is a data-gathering exercise, would you omit the majority of an innings from the records completely?
Someone who offers an edge on 0 and then makes 300 has clearly played better than someone who offers a chance on 0, makes 3 and then gets out. But according to FCA they played just as well as each other.
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Actually, on second thoughts that's not the biggest problem, it's just the most fixable problem. The biggest problem is that cricket is about making the most of the chances you're given at a quite fundamental level. Being out 'if only the fielder had held on to it' is essentially equivalent to being out 'if only it was hitting the stumps on hawkeye', for example. One's fielder error and one's bowler error, is all.
The batsman can't do anything to ensure the fielder drops it, sure, but he can't do anything to make the bowler give him a loosener outside leg stump either. His job is pretty much just making the most out of both.