Somehow my efforts to improve the urls seo technically (no deep directory levels) has failed. Google does not index most of pages.

The current structure of the website is as follow:

HOMEPAGE
index.php detects browser language and redirects with 301 to:
www.domain.com/en
www.domain.com/fr
www.domain.com/de

(default redirect is 'www.domain.com/en'; the last 2 characters defines the language)




OVERVIEW PAGE WITH LINKS TO ALL COUNTRIES
http://www.domain.com/countries (english)
http://www.domain.com/pays (french)
etc.




OVERVIEW PAGE OF EACH COUNTRY WITH LINKS TO ALL SPOTS:
http://www.domain.com/spots-greece-en
http://www.domain.com/spots-usa-en
http://www.domain.com/spots-canada-en

http://www.domain.com/spots-greece-fr
http://www.domain.com/spots-usa-fr
http://www.domain.com/spots-canada-fr
etc.
(the last 2 characters defines the language)






DETAIL PAGE DESCRIBING EACH SPOT: (on a separate subdomain)
http://spot.domain.com/spot-national-museum-en
http://spot.domain.com/spot-botanic-garden-en
http://spot.domain.com/statue-of-liberty-en
etc.
(the last 2 characters defines the language)



Is this structure "google unfriendly" or can somebody help me to improve the urls to get properly listed within google?

Somehow my efforts to improve the urls seo technically (no deep directory levels) has failed.
Google does not index most of pages.

That's because it has ABSOLUTELY NOTHING to do with how the URIs are structured.

Is this structure "google unfriendly" or can somebody help me to improve the urls to get properly listed within google

Search engines really don't care how your site URIs are structured.

How they are LINKED is what makes the difference.

Is your site new? If so, check your site's indexed pages across several search engines. If you get the same results with little variation, then there can be a problem. But if it only applies to Google, probably you are under the so called 'Google Sand Box'.

Also, some more info would have helped a lot. Such as whether you are using Flash/JS and such like.