I have some suggestions to apport:
I suggest that apport would show a message in the first step, not in the last 
step. So that the user would immediately know what's going on.
Also apport could allow to ignore some messages (the user would check to ignore 
them) and could support multiple messages (so that it would display a complete 
list of problem messages and would either allow to report them separately or 
all at once or would allow to somehow group them).
Also apport should distinguish among different levels such as WARNING and ERROR.
I think that implementing these suggestions would fix this bug (but of course 
upgrading BIOS would be still needed as the warning is not purposeless and 
Ubuntu can't upgrade the BIOS for you itself:)

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thinkpad_acpi: WARNING: Outdated ThinkPad BIOS/EC firmware
https://bugs.launchpad.net/bugs/554265
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