In last 2 years or so 18350 especially in IMR chemistry have become quite widely adopted compared to RCR123/16430 which rarely was adopted by flashlight makers. For 18500 FF(ones inside LP-E6) there have been quite a few improvements and now IMR cells can be found upto 2200mAh capacity compared to 1400mAh 5 years back. LP-E4 does use 18650 batteries so it would be possible for Canon to provide a tray(similar to AA tray) with their battery grips to allow users to use 18650 cells of their choice. Nissin has a flash that allows use of Li-Ion 14500 cells.the problem is not easily solved by Canon since they don't make cells and even the leaders don't do much in the way of development on the 18490's front (what is inside E6 batteries). Short of making mirrorless tech less power hungry there is little they can do without making batteries larger. 18650 get the brunt of efficiency improvements thus for multi cell packs I use them for building my own high cell count batteries usually due to cost to performance; such as for powering inverters for mains powered monoblock lights when I have no access to power outlets but a pack and head or SLA battery setup would be too big/heavy.
There are cells with better density such as 21700 and maybe 26650/26700 if you're lucky that are better for single cell style uses due to increased density from size but per gram/cubic mm they tend to be behind the 18650's on efficiency so at equivalent space multi cell batteries they still lag behind especially since they also cost more. The tech improvements does trickle into larger cells first from what I've seen such as substrate film manufacturing improvements to pack more electrolyte in given space and so on. As for smaller cells they don't see as much development and are limited in how much you can push them so not all developments translate down in length or width for various reasons I wont go into here. 18490 are a really minor formfactor especially and cr123 or 18350 are likely to be more popular before them and you barely see the big cell makers like samsung, sanyo, panasonic and so on update them never mind 18490's.
If canon released a slim grip sans controls that was basically just a battery holder with a decent BMS in it that allowed you to put your own unprotected 18650's or 21650's in I'd be a very happy man but I can't see them ever doing that really.