Do have the feeling that there is more bad guys than good guys in PoM?

Yeah you're right I think there are more antagonists than protagonists. Here's the list I made:

1. Dr. Blowhole- the penguins main enemy
2. Hans- Skipper's enemy
3. Officer X
4. Clemson
5. Savio
6. Rhonda
7. The Amarillo Kid- Private's enemy
8. Red Squirrel
9. Frances the Zookeeper
10. Vesuvius Twins

So far that's all I can think of, somehow only Skipper and Private are the only two have major archrivals.