The JAL flights from London to Tokyo and back really annoyed me last year because of padding. The LHR to HND leg arrived 45 minutes early, which meant I had 45 minutes extra of early morning time in Tokyo and 45 minutes less snoozing to try and get ahead of the jetlag.
The return trip was different, if the plane had departed on time it would have reached London at a time when inbound flights are not allowed due to noise restrictions. That meant it was about 2am by the time I was able to board the plane, again not ideal for sleeping.