First, I would give my first thought with sky islands; they can be a eyesore, as they are always visible from the surface, and below them, you have an issue with the natural light being quite lower. Having an archipelago design to them helps to make them have more unique designs (so they are not just overworld End islands), and helps make the individual islands smaller, thus prevent dark spots below them.
The cloud blocks seem fun, but while I get while leather boots help with powdered snow, I don't see how they help with clouds. Maybe feather falling can instead be used, where each level reduces the speed by which you sink in clouds by 25%, thus FF4 makes you able to walk on them. Maybe sneaking lets you fall in anyway, like scaffoldings do.
Skyslate seems nice at first, but I wonder if it is needed. Described as 'chalkier', it seems like diorite and calcite already got that for a bit. Also, maybe it is better to avoid the 'slate' suffix, as deepslate exists already, preventing skyslate from developing its own identity. Unless it plays on the theme that one is deep, and the other in the sky, both being extreme altitudes.
For the golden isles, I am not sure how good they really are. A gold tree already sounds like it gets close to bamboo in colour. I don't mind a new tree added with this, but maybe not a tree with a not-so-unique colour that is not even on all sky islands.
For the mobs, I don't really have much to say, aside from the Pegasus being a bit lazy, being just "horse with wings". The movement options could be kept for a more unique design. The rainbow fish giving the effect when eaten is a bit weird, if instead it could be used for a potion. Clockwork Golems seem useful with the ideas you mentioned so far, but be careful that they aren't too useful, limiting what future golems could do.
The cloud in a bottle, being a nice Terraria reference, is a bit odd. Nothing is mentioned about being able to bottle cloud blocks, so if they are only obtainable as sky ruin loot, then them being consumable for just one extra jump, no matter how high, is not worth it. Making the ruins generate potions of leaping already does something similar to what you look for.
I did have concerns about the natural shade created by Sky Islands, but I kinda decided that it's not something I can really do anything about. The lighting in the game is pretty lackluster in the first place imo, and light shouldn't be blocked 200 blocks below because of something in the sky unless it's REALLY big.
I just did Leather because the Cloud Blocks felt similar to Powder Snow. I don't like tying niche interactions to enchantments, so I chose that.
I'm trying to imagine the color. Calcite and Diorite are like WHITE, so Skyslate could have sort of a yellowish and grayish color to it. The names are WIP, but yes Skyslate was chosen to mirror Deepslate.
Bamboo is a very pale yellow while Golden Wood would be more vibrant. Maybe considering not having the "Sky Isles" at all and replace it fully with the Golden Isles.
Pegasi are awesome. Fight me o-o.
The Golems are going to be for combat almost exclusively, and they won't particularly excel in any area, just be very versatile.
Rainbow Fish were a last minute thing because I realized the Wellsprings had zero content, so I'll keep working on stuff.
I failed to mention I'm coming up with a crafting recipe for Cloud in a Bottle. I'm thinking of Bottle + 8 Cloud Blocks, but I'm sitting on it so see if anything better comes up. Jump Boost is cool but this would be way more versatile and fun to use.
Thank you for all the points, I'll consider them as I do more work on this.