Above all else, a stable editor.
I’ve been using Hammer since it was called Worldcraft and before it ever supported even Half-Life (was originally a paid Quake editor way back in 1997.) One thing that has always been consistent that it will crash without errors to the desktop randomly, resulting in work loss.
Even after getting anal with CTRL + S after every operation, some crashes can corrupt the map source file and result in total data loss or hours of work being undone if multiple backups are kept.
Another major issue is brush corruption, which became a problem with the Source version of Hammer.
Valve eliminated the CSG compile process (which converts vertex data to planes) and instead the VMF map format itself stores brushes as plane data. The problem with this is Valve didn’t use enough decimal precision to store planes, so if you make certain types of brushes with acute or obtuse face angles, the brush will become corrupted.
Since the VMF format calculates backwards (it makes brush verticies from planes), corrupt brushes end up creating several vertex points where there should only be one. Here are a few examples:
Notice in the top right viewport, all of the vertex clusterfuck. This was actually a single point when created, but after a save and reload of the map, the lack of precision caused the creation of many dozens of points all around the same area. You can see the resulting corruption as cracks in the brush junctions on the top left viewport where the yellow nodraw texture is visible.
Here’s another corrupt brush caused by using too acute of an angle. I think this single vertex became 9-12 vertexes. Each erroneous vertex can attach itself to a different face, multiple faces or no faces, resulting in bizarre effects. Like you can peel the corner of a brush apart by selecting different vertexes in the 3D view and moving them around. In the 2D views, all of the verticies are treated as one and will move around together.
Hammer’s error check feature won’t find this problem unless the verticies are too far apart from each other, but even if they’re not, these corrupt brushes can cause serious problems. The biggest issue is these brushes can cause clipping issues where the player can become stuck on a malformed clipping plane. It can also cause visleaves to be malformed, which cause visibility issues (like leaves not rendering properly from certain other leaves, resulting in null areas in-game.)