vmtCREATE and VTFexplorer are nice replacements for vtex. That creating materials is harder than in HL times is no surprize to me - they take much more time to be painted anyway, so converting them to the right format doesn't take significantly more time.
A -textureinclude command would be easy, yeah, and a batch compiler for simple textures, but besides that, it is just going to take more time. That's the cost of the better looks, imho. Not that I'm against easier, faster tools, I think better ones will be released eventually by the community (the community has already done a great job), but for now, this is what we got. Besides, I don't think it's even that complex or time-consuming if you invest some time in it.
EDIT: Pakrat does a good job including custom stuff bytheway, you can scan for custom content and autoinclude it with that tool. Sortof what you want with -textureinclude, but better.