OK, I forgot to include the 3do making, but the rest is personal preference. Frankly I like the smell :p
JKEdit has a type of layering, it's called the library functions. You export a "layer" that you named like in JED, but instead of turning off layers, it saves it as a seperate project which you can then reimport.
Honestly the MAIN problem wrong with JKEdit is the grid, which is why you don't see many good levels. Without a good grid, you just can't make the cleaves you want.
Weirdman, the best reason I can give you to switch to JED is the grid. JKEdit's grid is completely unreliable for complex architecture. It constantly shifts with each cleave you make and doesn't give you a wide choice of cleaving snaps. I found it near impossible to allign one piece of architecture to another. But with JED, the grid is unaffected by the level (unless you tell it to) allowing you to cleave at any angle, any position, any anything that you want. JKEdit may seem like the better tool right now, but eventually you will find out that complex architecture is extremely hard to impossible without the reliable grid that JED provides.
Sam: "Sir we can't call it 'The Enterprise'"
Jack: "Why not!"