WAD or PK3?

I dont really have much to say, just wondering on what the benefits/setbacks on wad files and PK3 files.

PK3 = smaller size and more organized.

a .wad file is superior for 1-map wads since you just simply need the map data stuff. .PK3 however is (probably) superiour in most ways. For one .PK3 allows access to 3D models outside of voxels, you can organise your textures/graphics into folders as well has scripts and is in general much neater in presentation. However, I do find .PK3 to be much more temperamental than .wad file usage...

I like .pk3 better. It's easier to organize and stay tidy. Not to mention, you can use 3D models in a .pk3.

You can never truly do away with Wads if you're creating a map. The map data, regardless of the map format (Doom, Hexen or UDMF) all have to sit inside a Wad, even if that Wad file then sits inside a PK3. So if all you're making is a map, then a Wad is fine. 

PK3s (which are limited to advanced source ports) are useful if you have lots of other stuff to include. They make it easier to manage things like textures, sprites and sounds, and introduce support for non-vanilla asset types like models and materials.  

So for any kind of advanced GZDoom or equivalent mapset that includes custom assets, a PK3 is the way to go. If you're just making a map and aren't including extra assets, a Wad is fine, because the map file has to go into a Wad anyway.

WADK3.

I don't think there are any practical benefits to the WAD format, other than that's what every engine supports.

I prefer WAD for single maps or small simple mods or patches. No need for PK3 for that. I'd only use PK3 for a huge project with lots of ends and outs. I'm old fashioned though so I still use WAD for most everything.