I think a lot of the general dissatisfaction on some features comes from people who have a LOT of alts. And on one hand, the counter-argument gets made that new players and free players likely have fewer alts to maintain. But it's not uncommon for games to offer gear or boosts to help alts out either. (For example, WoW has scaling heirloom items and double reputation for alts whenever you have one character that is advanced in an area.)
So I'd like to suggest this:
Have stores that unlock whenever you max a reputation or commendation category.
These stores sell account-bound consumable rep or commendation boosts and bundles.
The boosts act like the C-Store boosts (20% extra for the next 10,000) and cost EC. As in, maybe a million or so.
The bundles flat out award commendation XP or rep and cost dilithium. Something like 10k progress for 10k dilithium. Meaning that at a price of 100k dilithium, you could max out an alt in a category rather than regrind it. It's a huge dilithium sink but gives you an alternative to waiting and you'd need a character maxed out to do it.
For those who are going to put an awful lot of alts through the same systems, though, I think the least they could do, without doing all the work for the players, is to maybe, once you hit T5 in a reputation system, CXP category, or whatever, you get an accolade much like the Veteran ones, account wide, that boosts your progress through the system in question on all characters by say 20%.
It's not pay-to-win, it's a boost to ease grinding out progress you've done before without completely removing it.
The only issue I see with a permanent account-wide flat boost is that it would let those T5 characters leverage conversions (like CXP to Fleet Marks, etc) more often, but that's not terribly bad.
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The only reason I don't have alts, is that this game is so unfriendly to them. If there were things like this that made it easier to have more than one character, I would.
I can share your sympathy; as a player that have tons and I mean tons of alts, the current system is extremely unfriendly.
The PRO having many alts:
A) Obvious farming dailies - (At risk of severe nerfing)
B) Free Doff pack at the academy - (Soon to be eliminated)
Basically I will probably be stuck with tons of alts for just storage space.
A) Unfriendly system for those with more than 2 characters
B) Farming Dailies with all my alts will literally take close to 4hrs (Unrealisitc for me / time restraints)
C) Still have to farm for marks (Require lots of time)