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Oh, and the availability of same-faction BOFFs (and the cross-faction BOFF from the Diplomacy/Marauding DOFF rewards).... but if you are a DPS chaser, you will be using all Romulan BOFFs anyway.
but thanks. this helps.
Doffs are duty officers - they're used for duty officer assignments and Research and Development, among other things.
Cross-faction flying allows you to fly Klingon ships on Federation characters, and vice-versa. You can buy the cross-faction flying unlock in the C-store, or level a Klingon character to 65 in order to unlock it.
Whichever faction you pick, you will have access to their ships in addition to Romulan ships. If you have cross-faction flying unlocked on your account (Imperator mentioned how), you will have access to the opposing faction's ships as well.
So in terms of having access to ships, if you DON'T have cross-faction flying unlocked, then there is a difference, but not if you do.
You can also get BOFFs (bridge officers) from the allied faction, and ONE from the opposite faction (as a reward from the DOFF system)... but as I mentioned, if you are trying to maximize damage, you will wind up using all Romulan BOFFs anyway (the best damage trait there is, is Superior Romulan Operative), so this is not an issue.
That leaves faction-based access to locations and fleets. You will only be able to join a fleet of your allied faction.
And each faction has certain locations which are not accessible to the other faction (Starfleet Academy, Earth SpaceDock, Qo'noS, certain other planets)... but those are all social zones anyway, and all the vendors and interactable officers are identical (allowing for faction differences) except for one DOFF assignment that the KDF security officer has and Fed does not.... so this doesn't restrict you from having access to anything other than the locations themselves.
and also active duty ground and space slots for bonuses.
Federation (including Federation-aligned) characters and Klingon (including Klingon-aligned) characters cannot team up together.
At this point (given cross-faction flying as an unlock and other things) the only real difference between Fed and KDF characters is exclusive loot one faction has over the other via story missions (Plasma-Disruptor weaponry cannot be acquired by Federation-aligned characters with the exception of Fed-aligned Romulans), Elite Fleet Gear (Elite Fleet Phaser and Elite Fleet Disruptor are exclusive to their respective Starbases), and some hull materials using shields and vanity shields (Aegis set, Discovery vanity shield, etc).
There's a few other (relatively minor) "exclusives" but for the most part, yes.
(I.e. random-gen BOFFs being of different races, and the diplomacy vs. marauding DOFF assignments, and the security officer tribble carcass assignment.)
Probably the biggest difference, outside of fleets, is a handicap that Federation officers have that Klingons (and even Fed-allied Romulans) do not; it's not possible to get a second engineer BOFF (in addition to the Jem'Hadar one from the Gamma pack) with a damage boosting space trait, unless you max out diplomacy (so you can get a Nausicaan that way) or pay for the fleet Kentari or a lockbox/exchange BOFF. Klingons and Romulans both have unlimited access to damage-boosting BOFFs via their factional races.