For Europeans: Create a UK Ltd holding company, and a local entity for each country you operate in. Happy to answer specific questions by email (we're UK Ltd holding with local AT GmbH)
You can also save that local entity by moving the UK Ltd into your country and registering it in the local company registry (EU only) - great article on how to do this: http://www.internetszene.at/2009/03/31/checkliste-limited-od... (German, unfortunately)
What was your reason to do both a Ltd in UK and a GmbH in Austria?
We've registered an Austrian GmbH couple of years ago and haven't had any issues with that so far. The break-down of voting rights and shares are directly bound to how the common stock (usually 35k€ in AT) is being split. When it comes to investment rounds, the investors either increase the common stocks or buy it from the other shareholders for the nominal price (the percentage of the common stock value). The whole process is strictly bound to a formal process (a notarial act), which can get quite expensive, which is the only down-side in the long run.
On the other hand, Ltds still have some shady smack for some reasons over here (one is that you're seen as being cheap), so when you're an Austrian or German company, I bet you gonna need to explain as a small startup why you have gone the Ltd path when talking to big potential customers, and I think this is something you want to avoid at that stage ("act like how you want to be seen, not like who you are", and each serious company here is a GmbH). I understand that it's a big turn-off for young founders to put in 17.5k€ in cash from the start (which is the minimum amount to be provided when founding), but it pays off when it comes to reputation, at least when acting in the B2B business.
The simple fact that GmbH law greatly differs from UK/US corporate law makes it uncommon, and therefore cumbersome for any interested UK/US investors. Though obviously if you've got the traction they'll just bite through.
Also things like stock options, reverse vesting, convertible notes turn into overly complex issues when trying to re-create them in GmbH law.
And besides the additional bookkeeping/accounting burden, I have not encountered any issues with our current setup.
In regard to why Ltd+GmbH: We found the move-the-Ltd-to-Austria process a bit complicated, and also encountered the issue you mention, that people think of Ltds being shady/not trustworthy.
