I feel like I've done you a disservice taking so long to reply. The Emerald Isles was my all-time favorite levelpack in 1.09.4, and to see you taking the effort to bring it back and improve it has me pretty hyped, so let me give you my take on what I like to see in a level.
Levels that really mesh typically have a build up that's represented in both the level geometry and the game-play. Aquatic Labyrinth Act 2 is a good example of this. It starts off in a dark lower corner of the building it takes place in, and about 2/3s of the way through you eventually see daylight and the building from the outside, signaling both a change in game-play and how close you are to the end of the level. It's a small touch, but it can really change the feel of a level.
Well thought out enemy placement is an absolute
must in my opinion. Big open rooms with lots of crawlas are rarely enjoyable to move through, because the crawlas break the pace without doing anything interesting to the player besides being there.
Glaber's map in SUGOI Skytop Mountain Zone, is a good example of an open field with enemies done right. Moving close to one causes it to quickly zoom toward your location, so you have to be aware of your surroundings while running fast, AND while exploring. That kind of interaction makes both the enemy and the level a more memorable and enjoyable exprience.
In regards to the character trio. Some consideration should be taken into how easily Tails and Knuckles can just move over things Sonic needs to climb. Rooms with huge walls on the side will result in Knuckles just climbing to the top and skipping over everything if he's given the chance. A level that's only enjoyable as one character (when all 3 are allowed) is not a good one, in my opinion.
If you need an example of a level that tries to give at least Sonic an Knuckles an enjoyable experience, Sand Valley Zone in my level pack,
Digital Empire , was made with both of those characters in mind for just about every room. It's a shameless plug, but it's the first example that pops into my head.