Unfortunately, being incorporated in Malta just screams "shady business" - at least here in Slovenia where such companies belonging to questionable characters are constantly in the news.
I'm currently living in Austria, but operating out of my UK Ltd company. While it does work, there are a few pain points around banking, currency exchange and my residency in Austria (am I exercising my EU rights, living in Austria but still officially consulting for and being paid by a UK Ltd company?). It would make my life a bit easier to have an Austrian based company, but the amount of share capital required to setup a GmbH is quite high.