First, a level should be original, it should not be like other levels. Secret passages, warps, one ways etc. are really important to make the level interesting. A level shouldn't be confusing at all. In some levels the foreground is so confusing etc. Don't place ammo or food at places players can't reach. Use 'signs' to let people know where you can go through the wall etc.

Well, the ammo should fit the level (depends on tileset and layout) and there should be enough/shouldn't be too much ammo in the level. About the PU's, they are really important. I think they should be placed in corners of the levels, so people should move through the whole level. I agree with DarkSonic about the shape of ammo, be a bit creative.

About the flow, I think there should be always enough free space in levels. Some levels are really narrow at some places, I don't like it and never will, try to keep some open space, like three or four tiles, to let players move easier through the level.

I don't have much time now, but I will post something later or edit this one ...