So, I think that it will be easier to start out with an analogy, so bear with me.
If you blow up a ballon, let all of the air out, repeat several times, it becomes easier to blow it up. Luffy stretches his body when he inflates himself for gomu gomu no fuusen, but the bones were never blown up. That's the difference between gear 3 and the other techniques.
Thus, his bones were never used for inflation purposes and it may have required more effort to break through the boundaries from his bones. During the training for two years, he used gear 3 so much that they probably inflate really easily after their constant use, and that's why when he was in the bubble during the Kraken fight he used very little air.
This may be stupid or even already stated, but I really believe this is why he can use gear 3 so much easier now. I may be reading too far into this, but don't we all?