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.
Hopefully that'll pass some day. It's the same in Austria, however recently there's been new legislation for LLC companies with very low starting capital almost all over Europe, so you can have shady-looking businesses anywhere (e.g. 1-Euro-LLC in Germany).
Do you have some more information about that, specifically in the Austrian context?
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.
In Austria there were some initiatives to introduce a cheaper Ltd, called "GmbH light", but this was changed again. Currently there's a way to pay EUR 5000 immediately and EUR 17500 (total) share capital after 10 years ("Gründungsprivilegierte GmbH" - http://www.wirtschaftsanwaelte.at/gmbh-light-durch-die-gmbh-...) , but in your situation I'd be looking at setting up a german Ltd to get rid of some of the problems at least: http://www.ug-ltd.de/limited.html