Hi Harmy,
Have you looked into using CRF, rather than 2-pass encoding in x264? If you're not familiar with it, let me explain. Instead of simply setting an arbitrary bit rate, which may be great for one scene but under/overkill for another, you set a visual quality level. (CRF 18-16 and "slow" or "slower" is a good setting, IMHO.) X264 then decides what bit rate it needs to get you there automatically.
You can select different presets to speed up the encode. The slower presets will deliberate longer, but reduce your file size. Faster presets take less time to encode, but lead to bigger files. No matter what speed preset you select, the visual quality will be essentially the same (though there's some debate that the slower presets are a bit better), only the final file size will vary.
I've had great luck with CRF. You can read more about it at: https://trac.handbrake.fr/wiki/ConstantQuality and http://slhck.info/articles/crf .
I hope this made sense! Keep up the great work! :)