Hi Javier (and Hans),
luatex takes only utf, and if you want something else, one can recode each input line using a call back function to do the recoding (or use an external prog to preprocess the input), but mixed input encodings will demand adaption of the macro's used for (eg arab)
Of course there are a few things not implemented yet (in particular, we plan to have advanced support for in-line encoding/transliteration changes by making it possible to intercept the token builder, but that is not there yet). However, the practical problem is not so much unfinished things in the executable, but missing documentation and Lua script code. I'll be writing a section on input encodings for the manual tomorrow, and that should help clear up things. Please hang on for a bit longer until that is finished. Best, Taco