tl;dr: Focusing on account-wide gameplay and not character-specific gameplay will give Cryptic more money and benefit players at the same time.
Right now, extra characters are only valuable as an extra 8,000 on the dilithium cap. The main problem is that any real progress, mainly through the new reputation system, is limited to a single character. While the reputation system is generally an improvement from the past system, it's substantial enough now that, aside from a boost in dilithium refining, there's no real point in getting a new character. Extra character slots are less valuable, and will only continue to decline in value as new content is added, to the point where the number of people buying new slots will sharply fall. Making them more valuable would lead to more people buying more slots.
1) Make the reputation system account-shared. The reputation store can still be locked out until level 50 is reached on an alt, but there's no reason why the rewards of completing tiers in the reputation store shouldn't be shared across an account's characters, as that person has already completed all the content necessary for it. Forcing them to repeat the entire process every time they make a new alt is annoying and not worth the hassle.
2) Make all character-bound items account-bound instead. The only exception to this would be unique-per-character items. This will allow people to more easily outfit an alt, by buying items on their main character and transferring them over. Again, if they've already done the content and are able to reap the rewards, then forcing them to do it all over again just becomes annoying and boring.
3) Make the fleet leaderboards show total contributions by account, not by character. The same person has contributed, so why differentiate?
4) Allow dilithium and possibly fleet credits to be transferred using the account bank, like energy credits are. Pooling dilithium from the alts into a single character allows people to buy more. Right now the only way to transfer dil is to make a 25 dil/Zen buy offer, remove the offer, and then withdraw the dil using the main character. Again, this is annoying and tedious. Being able to pool dil more easily gives people more purchasing power, and makes dil a bit more valuable. The only problem I can see with fleet credits is the differences between factions, but separating fleet credits into Fed and KDF fleet currencies is a solution.
Doing this will not only make extra character slots more valuable, increasing demand for them, but will also increase demand on other Zen store items as well, since it will now be easier to make different alts for different situations. As an example, right now I have no desire to buy any fleet modules for a fleet cruiser or science vessel, because I would need to make a new alt in order to take advantage of that style of gameplay, which means repeating the 40+-day reputation process and fleet contributions. Again, it's not worth the hassle. But by making alts more valuable, now people are more inclined to buy things like new ships because they can fully take advantage of them. Someone can switch between an escort alt, a cruiser alt, or a science vessel alt based on what they need or feel like playing at the time.