Changes to [[Template:ar-noun]] and such
I was aware of that problem, but I'm not sure what would be the best way to fix it. To find a proper solution we'd have to ask, first, why we have transliterations for Arabic inflections but not for Russian ones. We should really be consistent. If we have them for Arabic, we really ought to have them for other languages too.
Maybe, but some languages are easier to read than others. Cyrillic is pretty similar to Latin writing so I can understand people not wanting to transliterate. Arabic script is quite different, and harder to learn to read because the letters have contextual forms and ligatures and such, so it's really very helpful to have the transliteration. I think you should put it back until we find consensus to do things differently.
Also, currently in many cases the transliteration has more info than the Arabic. Displaying the transliteration is thus important for multiple reasons.
You also eliminated the automatic vocalization, which really should be there until it gets fixed up with a bot.
In general I'm not sure why you felt the need to rewrite the templates in Lua; they were working fine before.