Another Mario Maker 3 Wishlist:

I've been doing some Mario Maker levels. I got I think 8 or 9 levels made. I still feel that there are some limitations to what Mario Maker can do in comparison to True Nintendo-made levels.

I have mentioned Extra modes like Mario v. DK levels (based on the GameBoy Donkey Kong game) or SMB2USA mode... or Doki Doki Mode for the Nihonjin. And the Wario Mode that adds Wario and Waluigi as playable characters.
I have mentioned looking at the SMLand games for inspiration... I'll try to not repeat those on this list:

More themes:
I know SMM 2 added some new themes making the grand total of 10 themes.
But not all the themes from the source games have been used. (Speaking only on SMB3/SMW here)
Ground covers the 1-1 style of SMB3 but not the 1-2 grassy style. Same thing happens with SMW. The Ground level looks like the demo mode in SMW instead of Yoshi's Island 1 or 2. So for the second "ground theme" let's call it Grassland.
Sunken ship: Basically a hybrid between Underwater level and Haunted House.
Cavern: a second style of Undergrounf that uses Lava tiles. Seen in SMW.
Mountain: This half underground half snowy area is based on SMB3's 1-5.

Water tiles: pools/waterfalls
The rising/falling water levels from the forest are a neat addition, but they don't capture the full potential. Waterfall tiles (could also double as quicksand on desert levels.) Can create some high tension situations. The waterfall drags you down as you attempt to climb a vertical level. Pools on the other hand would be standing water. Combinations of these elements could allow players to create wet/dry levels without requiring pipes for a Water sub-area. Before anyone asks, yes, the Super Mario Land 2 sap areas were part of the inspiration.

Theme specific bosses:
We have Bowser and the Koopalings as generic bosses. Boom Booms too! But these guys would be End Stage Boss types, meaning that only by beating them, the stage is cleared. This status can also be applied to A Boom Boom, A Koopaling, A Bowser or Bowser Jr.
Well how about a Boss that is different depending on the area:

KING BOO: an oversized Boo who requires 4 hits on the crown (stomps, throwables) who only appears on Haunted Houses or Sunken ships.

PETEY PIRANHA: An oversized walking piranha plant that requires to be stomped when it's not attacking. Grassland and Ground seem to be his favorite areas.

TATANGA: An Alien invader whose Spaceship behaves like a flying Boom Boom. 6 hits shall send the alien packing. He'd appear on the Sky stages.

MEGA RHINO: An oversized Dino Rhino with behavior similar to a Dino Torch from SMW. This mighty creature hides in the Desert.

DONKEY KONG: Mario's pet ape has a bone to pick with his owner. Only throwable items can appease the ape. He'd hide in the forest. Wario's pet Yeti Wonkey Kong hides in the Snow and Mountains.

DRY BOWSER: a Skeletal version of Bowser haunts the Castle.

Nintendo can figure out the rest.

Alternative springs:
We currently have either Noteblocks or SMW style springs. I would like to see the SMW diving board style.
Big unmovable springs (inspired by the High Jump springs from SMB1) with a higher jump power.

Jumbo stage elements:
We have big enemies, but not Big Pipes, Big Blocks, etc.

Boss Door:
There's nothing more annoying than setting up on killer boss battle that gets screwed up by accidentally pressing up in front of the door that brought you into the boss room. So, this limited to one per level Boss Door would take you to the end of stage boss room. Just make rhem work like the 3d world warp boxes.

Throwable items:
Just as the name implies, more items that Mario can grab and throw, or in SMB1 mode's case, kick. Empty Koopa Shells (or blue upside down shells in SMB1 and SMB3 modes) the Snowballs are quite the innovation, but only useful in snow levels. Also Spiny and Buzzy Beetle shells are wearable and people manage to screw levels and get soft-locled by wearing them. The empty Koopa Shells avoid that. The White blocks used by Buster Beetles would be also a nice addition.

Chain link fence:
A SMW staple, it adds a pseudo 3d element to a 2d game. Some exciting levels can be made using this dynamic of alternating between foreground and background.

Mario Brothers levels as bonus stages for World Maker:
Instead  of devoting a whole new game mode I think these having these as an actually playable bonus stage would be a nice feature to mix things up with the Toad Houses. It's also a nice throwback to Super Mario 3.

And I believe this is all I can think of for now without retreading into prevous rants.