Translation:What is the mode of transport that you like most?
"Favourite" is like "optimal" or "maximal", they are superlatives in themselves, meaning "most preferred", "best", "biggest" respectively. "Most favourite" is bad language.
I can't shake the feeling that there are many native English speakers that would say "Most favourite"
"What is your favorite mode of transportation?" is a better English sentence.
"Apakah alat transportasi yang paling kamu suka?"
Translation:What is your most favourite transportation mode?
What transportation mode do you like the most? = accepted.
What is the transportation mode that you like most ? = not accepted, reported.
What is the transportation mode that you like the most ? = not accepted, reported.
"Transportation mode" isn't really something we'd say in English either.
"Mode of Transport" and "Method of Transport" are better.
What is your favorite means of transport? What is the means of transport that you like most?