I've always believed a good multiplayer level should focus on "paths". A path is any route that a player takes between key points, such as carrots, CTF bases, and powerups. They should feel natural to the player, and be easy to navigate.

All paths should connect to other paths in some way, so dead ends should be avoided unless they contain something very important (like a base). Even then it's usually more fun to avoid dead ends. Note that I do not consider something like the bottom left of battle 1 a dead end, because even though you can only exit it from 1 direction, you can enter it from 2, and also players generally don't go to that area unless they are passing through or setting up an ambush.

Finally, to make gameplay interesting and dynamic, paths should intersect occasionally. This is where the "X" design comes in. The centre of the level is one big intersection, with several paths branching off of it. Presumably, the ends of the "X" connect to each other in some way, perhaps through tubes or warps. These intersections often form "hubs" where a lot of gameplay occurs.

The "X" design is good because it focuses on a central hub, with a bunch of paths branching off. This kind of level is easy to design, and also feels natural to players, so it is no wonder why a lot of good levels use it.