* Make a server component to be able to identify which clients have downloaded which update. And how many had installed the latest version in a period of time (you said that probably will be included in the next version)
Trial tracking & specific feature usage tracking is being included in LimeLM. If you just want a broad-strokes tracking the tools are already there (logging, passing product keys to your servers alongside the check for update, etc.).
* Ability to erase no longer needed files (you said no)
That's correct. wyBuild actually needs the files to generate patches. It can't "remember" what to do to make a patch (that's why it needs an actual file on the disk). And very large hard disks are dirt cheap.
* Ability to edit configuration files at least for xml files or .NET config files (you said no)
If it was possible to do in a universal way, we'd jump on it. But it's not possible short of programming an AI into wyUpdate. Even then it wouldn't be accurate. Hence, FAQ: What's the best way to update config files?
* Improve the Integration with an automated build processes to make it simpler and avoid the need to alter the config files for each release (what's the point of an automated process if you had to do a manual step every time) (you said that you already had one process and won't change it)
wyBuild build automation is merely a step in the build process. It's not the entire process. You need to use something (like a script) to generate the XML file that will be used for the update so wyBuild actually does what you want it to do.
Unfortunately wyBuild can't just guess what you want and do it. People still have to tell it what to do. And in the build automation that "telling" is generating an XML file for it to use.