I signed up here just to say I
had the same problem on my rooted Note 3 (SM-N9005), KK 4.4.2.
I decided to take a look at my Snapdragon's speed at its most dormant.
After installing 'No-frills CPU Control' from the Play Store and raised the slowest frequency from 300Mhz to 652Mhz (see attached screen), I haven't had an ounce of skipping. The additional battery drain has been negligible.
As the above comment mentioned their success in using an Exynos, I'd say Samsung and the like are dropping the Snapdragon speeds too low in order to claim better battery life; this is however having a detrimental effect on BT when the screen's off.
Anyway, this is the experience I've been having and it's paid off! Give the CPU a nudge and let me know how you get on.