I'll start!
I wish the Alchemistry kit held the completed powders as well as the compounds. I make the powders one at a time and never have any compounds leftover to make the Kit useful.
I wish ONE OF THESE was the default instead of ALL OF THESE. I really, really wish this one.
I wish all the common harvestables stacked. Grain stacks into bundles. Why don't eggs stack into crates, cherries into bushels, milk into tanks or vats, beans into sacks or cans, paper into reams, gas into barrels or canisters, wood into cords, etc.?
I wish the Butterfly Milking message was less intrusive in chat and in the black update spam boxes. I wish the black update spam boxes could be toggled on and off. Milk six butterflies, 2/3 of your screen is blacked out with an annoyingly long milking spam message no one reads after the first 1000 times you see it.
I wish the animals, especially pigs in pens, could be briefly frozen or herded to prevent the usual ZERG RUSH behavior that makes it difficult to select the ones you wish to pet or nibble.
I wish we could DO something with the gems and that there was a greater variety of them.
I wish Global Chat would stop disconnecting.
I wish there was a way to use your house as a place to replenish energy, even if it required purchasing a special object to get the ability.
I wish my cabinet, trees, animal pen and garden area were lockable. Or that doors to the upstairs and downstairs and the ability to leap off of balconies could be toggled on and off.
I wish that we could combine all the music blocks together to make a jukebox.
I wish the cubimal bag held all the cubimals available.
Because we can't remove sad chickens or butterflies whining about overcrowding, the nagging about how sad they are is unnecessary spam. I wish we were able to relocate them, or turn off the nagging.
I wish there was a way to check whether or not you were about to waste powder on a shrine because you were close to going over your daily donation limit for that Giant.
I wish that mine-able rocks were a higher menu priority than tombstones and mail frogs.
I wish the wishing well feature at Baby Steppes in Ix DID something.
What are some of your wishes?