I'm going to list all the problems I have encountered that I have noticed so far and comments. They aren't really in any particular order, just as I remember. These will include some previously mentioned hot topics. Please keep the comments G rated. Compensation Gear.
I think this is a problem, unfortunately, the only way to fix this is to allow players to catch up. I believe that is the intent of 6.5. Soo, the only thing I have here is can we have 6.5 sooner please?
  Enchant Rates
Rather disheartening and annoying. Again, 6.5 patch thing.
  Skins
I know the focus is on transforms. But I really hate many of the starter set skins (haven't gotten the later ones). I would love to have skins back available. Possible places to get add them include: Luna Craft, Lifekeepers (E)/ Veilbreakers(A), BCM (obv.), crafting, and the GST. 
  Golden Sand Traders Skins
Please expand this. Most of the skins there are awful. I believe you have stated you are working on it. I'll be waiting.
  Golden Sand Traders Shards and Transparent Transform Scrolls
A step in the right direction, but as mentioned extensively, these prices are stupid. I am not even interested in either of those, and I still think those prices are dumb. I think this is a relatively easy fix too. I think when you update the Gold bar shop on 12/5 would be a great time to implement these changes (you are updating the shop, right?). 
  GST Shard bundle
Asmo character does not have them on the list to buy. Elyos character does (same account, different server).
  Siege Lag
Dunno how much you can do about this. but getting 300 to even 8k+ ping in the US is ridiculous. If you can do something about it, it would be much appreciated so I can fully participate.
  Glory Points
As of right now, glory points are really stunted. I know you guys have done some to fix this, But as stated before, the only progression is through people not meeting the requirement. and it almost seems like that requirement is being at most if not all sieges. I agree that GP should be PVP only, but I think the current gains are not enough. My personal opinion would be to completely reset GP and maybe increase the gain so competition is better. (JFYI not even an officer).
  Siege Timings
I know I'm going to get a lot of flak for "US game. US target", but really, it's more than that. Siege is the only source of conquerors gemstones that I know of and a major source of PvP Enchant stones. It's kinda kneecapping the non-US population in a way, and I bet there is a fair amount of people in that group. It would be worthwhile at looking into modifying siege times and/or occurrences as I think it would benefit a significant portion of the playerbase. Do I think it's easy? No. You have to juggle like 10 timezones at massively different times. I do think it would be worth a try, however.
  PvP Enchantment Stones
The rate of acquisition of Legendary/Ultimate stones is appalling. I don't think I've seen an Ultimate PVP stone yet honestly. I know there is an upgrade exchange coming in 7.0. But that's a long way off. any chance we could get that sooner? Make ancient PvP stones more relevant. Additionally, you could increase the acquisition rate in PvP activities.
  Dredge Rewards.
As much as I like bum-rushing for the stones, I would prefer it to be different so the actual focus is on the instance, not rushing to X for Y reward. My thought is to move the rewards back into completion rewards. Naturally award more for winning. Heck, even make an extra bundle for defeating the captain. My thought is 1 dredge bundle for losing containing 1 random enchant stone bag(contains multiple stones) and maybe a conquerors gemstone, 2 dredge bundles for winning (same contents), and lastly a guaranteed legendary stone bag for killing the dredge captain. The last bag would not be a lootable drop, but again an end of match reward. This is in place of current lootable drop rewards. AP acquisition would stay the same.
  Crafting Levels 60/160/260
Why is there not a craft for these levels? It makes x40-x80 excruciating nearing x80 (like 12+ crafts per level.) Is this better than 5.8? Yes. Were materials more available in 5.8? Arguably yes.
  Crafting material availability
With bots around, it is harder to get materials now. Plus needing 5 per codex is kinda annoying. Especially when it then takes multiple codex per craft and multiple crafts to proc. Add in the extra price of the scrolls required to craft and it gets expensive fast for not a lot of payoff. Could I request a lowering of materials needed for codex? I understand it's not supposed to be easy, but if you are levelling Aetherforging from 0 it's can take quite a long time.
  Crafting Stone Disenchanting/Upgrading
2 higher stones for 1 lower stone? really? this should be the other way around or the typical 1:3 ratio we used to have.
  Crafting Purpose.
It seems it's really only for the ultimate placeholder pvp gear and maybe legendary pve gear (until you get instance gear). Can we get more useful crafts that will mean something?
  Screen Splashes
Cubic Lab could be smaller, but is otherwise fine. All the chat and screen splash spam from people getting stuff from instances, plussing and upgrading is annoying though. Especially since it's the ENTIRE server. I don't care what  xXProfightsXx or whoever got from IDD today. I'd rather it not pop in front of me, especially since PvP is common in Lakrum. Please? This is similar to the Abyss crap last patch, just less frequent and less prominent. (if your name is xXProfightsXx, I'm not singling you out, I just picked a name)
  PvP instance timings and entries.
More please? I know there are big windows, but with the amount of AP you need to upgrade and to get Fighter Fragments, it would be nice to be able to do PvP instances more. 
  Lifekeeper/Veilbreaker coin requirements.
can we get these lowered please? Grabbing the legend wings/bracelet/plume would be nice if it wouldn't take literally months to do. (assuming an average of 10 coins a day, that's 70 days or 10 weeks PER item on average). 
  Ultimate Kibrium availability
I don't know how often the World Legendary Boss spawns, but I've only seen it once and I don't remember when. It does award a fair amount of Kibrium for defeating it, but considering both factions are fighting for it, it would be nice to have a second way to obtain it (luna dice doesn't count). Oh, and don't put it in high end instances, that would defeat the purpose. Luna Weekly might be a good spot to put it. Something to consider.
  Minium
For those that have Grade A or B minions, I feel like lower grade minium is basically useless. Considering you can get B grades from instances, upgrading C grades is...kinda useless in my opinion. I would like to see if we could get an upgrade exchange. As for rates... not entirely sure. maybe 10:1?
  Guestblooms
Make guestblooms available again. I wouldn't think it would be too hard to reimplement the vendors (since some still exist) and update the rewards from the Guestblooms.
  Housing Item Availability
As has been mentioned, previously available housing items have disappeared with the patch. It would be nice to be able to get them again. Kinah is fine. Petals is only fine if you fix getting guestblooms.
  Teleporting to Lakrum
Why is the house port only one way? I would also like to have the Academy port be both ways again too.
  Eye bug.
Would be nice to have this fixed. I understand you are working on it. Just don't make it an NCSoon™ please.
  Invisible Walls/Terrain Glitches
There are glitches in the terrain that cause seemingly nothing to act as if it is an invisible wall until you jump over it. The most annoying is the Lakrum teleport pad elyos side. I have encountered this in the Temple of Records once or twice as well.
  Super Saiyan Idle Animation. (IDK what it's actually called)
Firstly, the base animated stance looks like the character is trying to poop. Hilarious in a way. Secondly, holy nyerk is it annoying. Especially when there are multiple people on the screen that have it. At a minimum can you make it NOT shake my ENTIRE screen? Thanks! I'd appreciate not having the glow/whatever have such a large footprint as well.
  Lakrum Mob Availability
I believe the spawn rate was increased already, but it's still pretty bad in some parts. As I have mentioned elsewhere, I would be agreeable to a small increase in density of mobs or an additional increase in spawn rate.
  Luna Rewards are still wrong.
Luna Blessing was removed a while ago..
  Mount Availability
Being able to get permanents without going through the Luna Dice roll/BCM would be nice. 
  Things not saving to skill bars
Namely pets and minions, but I have been having issues with things not saving when I move them or put them into my skills bars.    Will add as I find more.  Do I expect these all to be fixed? Nope. But I can at least bring them up. Also @Cyan, have you considered starting an FAQ of sorts?