Looks that way yeah...
What it really boils down to, is this:
Zen Ships (Formerly C-Store): Grind Dilithium, or pay flat-cash, get ship instantly (account-wide). Ship comes with extra console (bonus ability)
Fleet Ships: Grind Dilithium and a bunch of other things, wait several months to get the shipyards upgraded, purchase of ship requires an extra module (or 4) that is purchasable from the Zen Store, or off the Exchange for millions of Energy Credits. Ship is unlocked per-character (NOT account-wide)
Ultimately, what it comes down to, is that "Zen Ships" have slightly inferior base stats such as Hull and Shields, but they get the extra console ability, and the ship is unlocked account-wide. "Fleet Ships" have superior base stats, but no extra console ability, and the ship is unlocked on a per-character basis. Not to mention, the extra time and work involved, in grinding your Fleet Starbase facilities to allow the purchase of the "Fleet Ships".
TL;DR: Season 6 is 2 days old, and already it's been a colossal failure in my opinion. Season 7 will likely be my final season in this game, then i'll move onto "bigger and better things".