dkna
Oh yes. For instance, LuaTeX doesn't print combining diacritics correctly unless you painstakingly swap the underlying codepoints around in some unspecified order (to be determined through trial and error) that doesn't match _any_ of the Unicode normalization forms.
Good thing you didn't bother, because it's absolutely not worth it. I chose LuaTeX initially precisely because it seemed more convenient to write commands in Lua than in plain LaTeX, but it turned into a total nightmare. Issues crop up as soon as you try to do something with text that embeds LaTeX macros, and the errors you get are even more byzantine than the ones you'd get by writing "normal" LaTeX code.
IMHO the very idea of embedding an external language into LaTeX is pointless, for the simple reason that LaTeX isn't markup, but code, and that it's pretty much impossible to parse it into a representation that makes sense and could be manipulated like, say, the HTML DOM. The only sane way to automate things is to write your documents in some language or markup that can be compiled to LaTeX, or to use a template engine.