I'll update this whenever I find new things to whine about.

Green=New, No Response
Yellow=Response, Being Fixed (or Fixes Being Attempted)
Red=Response, Not Being Fixed (Typically the Pettiest of the Petty)
THE GALAXY
Empty Space: Yes, space is a big place and it is generally filled with nothing. But some systems have too much nothing, overly conspicuous amounts of nothing. Borleias and Fresia for example just have the one planet and a handful of orbital stations. The Gamor system has nothing, literally nothing, in it. Why can't there be an asteroid field, hidden bases, wreckage, or the occasional parked NPC capital even? Exploring is fun, but unfortunately everything is already marked on the map for us.
Where Are the Light Freighters?: NPC freighters like the YT series, Lambda Shuttles, Cargo ferries, etc. are all notably missing from the game. Whenever I enter a system it is massive BFF-1s and Container Transports as far as the eye can see, and they all belong to a large corporation too. Where are the intrepid self-employed captains of barely spaceworthy pieces of crap that define the Star Wars universe? I have seen the U&A YT being flown by Czerka and XTS but that is it, and it makes me sad.
Golan Guns Removed to Make Dance Hall: It is common knowledge that the New Republic's Golans were fixed and they are now quite effective at killing things. Funnily enough however, Imperial Golans still do not work. We wouldn't have noticed this before because we were never attacked and NR ships never really got near them as far as I can remember but as it turns out it isn't that the Golans aren't firing on hostiles, they just don't have any guns period.
Golan Equipped with Plot Armor: A side effect of arming the golan stations is that balance tends to be heavily skewed toward the defenders if tone of these stations is present. Although Golans certainly have a lot of firepower and should be utilized by the defenders for extra firepower they should be counter-able and they currently are not. This is because they are freakin' invincible. These stations have more firepower than an Imperial Star Destroyer and are invincible. It's a tad bit frustrating. If they can't be made destructable maybe tone down their firepower so ships can survive when near them for some time?
Countless hit with Space Delusion Sickness: Whenever I spawn a hyperspace hole, while waiting for it to stabilize I've noticed that the AI's mind is blow by its appearance. Some, like the New Republic, find it a hostile object; as such, they send barrage after barrage into it aimlessly (mind you, my character is listed as pro-GE, so I would contribute the fact that they attack it to such a reason). Others, like many of the freighters (at least in Bilbringi for certain) find it the greatest thing since sliced bread, and can't wait to jockey for sitting right in the middle of it! Now, I like watching 5 freighters try ramming into each other as much as the next guy, but enough is enough.
DATHOMIR
Martians Are Invading Star Wars: Why is Dathomir a terra-formed Mars? Why are multiple other planets terra-formed Mars too? Why is Hawaii located on Calamari? I know the planet skins are old but now that I've noticed what they are I can't stop noticing so everyone else might as well feel my pain.
UPDATE: This is now a highly petty argument
FONDOR SYSTEM
Shrink Ray Used on SSD: Them Imperials testing their super weapons again. Although why they tested it on their only remaining Super Star Destroyer is beyond me. Maybe that guy from the Death Stars' planning committee was there. I hate that guy. Anyways the SSD is much smaller than it is supposed to be. This is ignoring the fact that scaling it to the proper size would mean it would dwarf the planet it is orbiting. Stupid scale issues.
UPDATE: This is now a highly petty argument
Super Star Destroyer Stripped of Weaponry: The SSD also lacks guns. Do I think it needs an SSD's full armament? Lol no. But the ship should have some firepower, at least enough to repel lone capitals that get cocky.
UPDATE: This is now a highly petty argument
FRESIA SYSTEM
Rebels Sneak Past Sector Defenses, Again: Yes this is a petty argument. Before Borleias was annexed by the Empire NR NPCs spawned in Fresia because it was a contested system. Now Fresia is effectively behind the Front Line but is still seeing frequent attacks by NR fighters which could quite frankly be put to better use elsewhere.
Incom Supports Rebels Despite Being Imperial Owned: Well, it wouldn't be the list of petty annoyances without these now would it? Canonically Incom did make the famous X-Wing fighter, but the team that did that also sort of defected. Fact is Incom was always an Imperial company and remained Imperial aligned through this time period, more so than ever thanks to threats of force and actual force. The group that brought you the X-Wing moved on to found FreiTek and bring you the E-Wing. Incom made the I-7 for the Empire. So why are all Incom ships buddy buddy with the NR? It's a conspiracy!
KASHYYYK SYSTEM
Hutts Continue to Nuke Things: Hutts are still spawning in hostile to civilians, Imperials, and I presume NR in the Kashyyyk System. This is a little bit of a pain because they spawn in next to the Calamari jump and Hutt ships are crazy well armed. A YT's shields just drop in a few second and if you didn't slam the cruiser engine it is as good as dead. This obviously isn't just a pair of hutts but a lot of them. Maybe if there were less spawning in?