I'm what you may call, a pro snipah, I'm currently S+69 (lol), and I got to S+ only noscoping scrubs. So I think I can lend my mlg advice here m80s.
Jokes and mlg comments aside, I personally couldn't choose between these lovely weapons, but if I had to pick one over the other I'd pick.....
The vanilla.
Here's why: The burst bombs have a nice synergy going with damage up, which enhances your close combat/mid-range abilities. Damage up helps the main weapon get partial charge OHKOs, which is helpful as it conserves ink, and helps you kill much faster.
Damage up on the Custom only benefits the main weapon, unless you thought your kraken wasn't doing enough damage.
Another reason is for gear slots, since damage up is a must on any E-liter class, you'll be limited putting other abilities on your build. So, you might want to redirect these abilities to the weaknesses of the weapon, the poor mobility or the insane ink consumption.
With the custom I feel obligated to use at least a main of swim speed, as it helps the kraken get more kills in the heat of battle. Also getting a kraken (at times) can be rather difficult. Therefore, running tenacity or some special charge up might be wanted as the main weapon can't ink turf that good.
Meanwhile with the vanilla, I can run ink recovery, ink saver main/sub, and still feel good about it, as not having swim speed on this kit doesn't affect game play as much.
With the added ink recovery that I can afford on the vanilla, and the useful instant refill of the echo I can take much more shots than the custom version could with it's swim speed.
To those saying "OMG, burst bombs got nerfed u scrub, therefore u can't use them because they can't dew anything anymore. git gud u nub".
Burst bombs are still extremely viable, 2 direct hits still kill, and with your damage up your 2 hit kill only gets wider from there. Also burst bombs do something a custom E-liter could never do: cover small patches of enemy turf quickly.
Also not to mention burst bombs can help you escape in hostile territory. If you wanted to do this with the custom, you would have either died or wasted your special.
Overall though, it still comes down to preference. If you like the kraken for it's close combat potential, and if you like the beacons that allow your team to get back in the action quickly. Go Custom.
If you like burst bombs that help you cover small patches of turf, echo for spotting enemies, and a bit more gear independence, Vanilla is the way for you.
Sorry for this long post, I just have a passion for chargers in general, and I have some great experience with both weapons. Both weapons are clearly extremely good in their own right, but I just prefer the Vanilla version a tiny bit better. I hope this helped your conclusion on which is the better charger. ;)