Looking back, I think it must have mainly been a mix of the ZScript and lump management requests/demands and the complaints about the new texture browser. Personally, I've been more than content to use SLADE 3 for the lump management and then the one-click process of importing changes to the resources into GZDoom Builder.
Actually I think there are legitimate reasons to complain about the new texture browser. I actually rolled back to a previous version because of it. In the old browser, I work with small (64x64) images for each texture, to allow me to browse quickly through a large number of textures if desired (this is also how I use the Worldcraft editors for Half-Life and Quake), and they work fine. When I upgraded to the new browser, I found that this approach didn't work; many of the textures showed up as "X" and so I had to choose between increasing the image size substantially, or letting it display texture previews proportionately to their size. The folder structure may have been an improvement for people who put their textures in folders, but as I don't have my textures in folders I found it primarily an inconvenience. I didn't have a significant issue with the grey boxes around the textures though.
The complaints could quite possibly have been worded better/more constructively, but nor do I like, when a change doesn't work out as well as intended, the approach of minimising others' concerns and telling them to get used to it. Ultimately, if people complain too strongly the developer may leave, but if the developer goes ahead with changes that too many people don't like, it could put off a slice of the user base. Hopefully MaxED will return or someone else will take up the reins at some point. In the meantime I'll be sticking with GZDoom Builder version 2.3.0.2711.