The island to the left has a good amount of detail and isn't overcrowded. However, it looks a bit strange having the green paths separated since I'm sure that when the events are revealed, they're going to merge. There are tiles you can use to mend them. It's a little bothersome how on some of the hills, the top part of the shadow doesn't line up quite right with the lower part of the hill's shadow, so you may want to either just use the eyes on the hills or redraw some tiles you're not using so you can have hills with perfectly-aligned shadows.
The island to the right looks like it's in very early stages... :-/ I'm not sure what you're planning to do with it yet, but you should flesh out both islands (hint: sort of like how you did below the fortress) so that they seem a bit more natural.
I'm pretty certain you have the lower left-hand corner reserved for Atlantis, and the exit on the right island goes to the underground. If I recall, the first world had a lot to do with pyramids, so I'm wondering if you're going to add pyramids to the left island - it's cool to see pyramids in places other than deserts.
Don't be afraid to use more space in the lower right-hand corner. Also, ExGFX80-FF are useable on the overworld, so you might want to create new tiles for your Atlantis submap since very few things from SMW's OW tiles will look right for an underwater city.
First screenshot looks fine, but I'm a bit wary of that koopa - if he's using the top-right tile that's normally blank on a normal GFX01, then it will mess up the score tiles when you hit a block with a coin in it (you'll get garbage before the number.) You may want to use ground bushes as well to break up the monotony of the ground.
In the second screenshot, I like how you're mixing tilesets to give the illusion of there being a sand mound inside the structure. I'd suggest moving background palettes to palette 3 so you can fix Mario in the status bar. (In the Map16 editor, change the BG tiles to use palette 3, then copy+paste the colors in palette 0 to palette 3, and copy the colors of palette 0 from a level with an unmodified palette and paste them on this level's palette 0.)
In the last screenshot, I can see you're using NES rips - it's not a good idea to stick with the NES's colors, though, because you should remember - the NES could only have up to 4 colors on a palette per tile, whereas the SNES can have 16 (usually 15 + transparency.) You can change around the palettes a little or redraw them to smooth them out, like changing the outline of the curvy stripe to an intermediate green, and using a slightly lighter shade of green to anti-alias it, and changing the black shadow to look like a darker shadow with the ground pattern continuing. The sand should definitely not stay orange - change it to a more brown color so it's not as eye-searing. Also, don't be afraid to completely recolor that brick.
Lastly, it might be a good idea to widen the pipe so there's no empty space between the pipe and whatever it's up against, such as lava or water. ;)
I'm glad you're still working on Mario the Archaeologist. It's a hack that truly dares to be different, and I'm eager to play both parts of it.
Just look above you...
If it's something that can be stopped, then just try to stop it!