Not sure if these have been said yet but gonna go ahead and post it anyways (I believe some have been stated before).
Increase what you can reclaim with AMAN Vouchers:
Guild Points
Nyzul Isle Tokens
Zeni
Ichor
Voidwatch Stones
Heavy Metal Plates
Dynamis Currency
Riftdross/Riftcinder (even if its 5:1 trade)
Home points in Beastmen Strongholds in the past by the BCNMs, in Halzam Testing Grounds
Decrease timer for Assault tags as your rank goes up
Show the decimal point for crafts and skills
Be able to warp to beastmen strongholds in the past from towns
Trading 3:1 limbus upgrade items for an item you want and/or buy the ones you want with ABCs
Make empyrean weapon upgrade items non-exclusive (can exclude souls because of demand and possible monopolizing)
Being able to be apart of multiple crafting guilds at once for points
WKR/Delve Gun (bullet from hurkan doesn't count and X-bow from Shark doesn't either)
Allow to get multiple stones from NPC for skirmish at once instead of one at a time
Unlock Relic WSes so that they can be used with or without the weapons
Please please please add ToAU, WotG and SoA jobs to relic weapons; I know its been asked before, but its only fair (would love to use Mandau on DNC!)
Change Gungnir's Aftermath, shock spikes is so hate'n
Change Einherjar's time limit to 30 minutes regardless if there is under 6 people, people are not gonna waste time being in there, its a get in and get out thing.
Make Reforges for Abjuration gear and Salvage.
Be able to go into beaten mission fights for fun. Also make it so on CoP mission fights can choose to have level cap on fight or not (the idea of doing "One to be Feared" with the level cap for the fun of it brings a challenge back that can be done again.)
Make ToAU Kings (Khimmy, Hydra and Cerby) pop NMs. You get the items from the ISNMs and then those Kings have a chance to drop a higher tier pop for even better items
Remove runic portal animation along with Magian moogle.
Remove tally wait for Ebisu Rod
Uncap the rest of merits; with Job Points becoming mandatory/necessary at this point, being able to merit everything shouldn't effect things drastically.
Decrease wait time for relic stages, totally unnecessary in this day and age; JP midnight is at the most acceptable
When getting Campaign tag ask automatically if you want in a Union
Make Campaign like Reives where you get performance evaluations instead of having to take off your tags
Add a guard stance on mnk where you get high guard rate and some PDT but can't counter while active
Adjust drop rate of Crystal Petrifacts so they drop less; having a chest that has 3+ in them is uncalled for
Make Magian Trial Weapons upgradable to Ilevel, only thing this system is really good for at the moment is for empyrean and relic armor and REM weapons