I'm having trouble finding information on a suitable replacement for the Yún with long term support since it is being retired.::::SNIP::::
@ngmarduino,specifically, nginx or Apache is not recommend as a webserver - both are too blotted. There are other alternatives. I'll let others make suggestions, however bottle is very popular with developers.
Jesse, a very nice summary of the current situation! Just to be clear, bottle is not a web server, it's a web application framework. It does have a simple web server built into it to support development efforts, but it is not recommended to use that server in a fielded application. In real life, it is designed to run under a more robust web server. That web server could be nginix or Apache, which are often more powerful than needed, or it could be the native uhttpd server that is the default server for the Yun.::::SNIP::::