Holland has some very good tax breaks for start-ups. To encourage innovations income from innovations is taxed at 10%. Also if you a foreigner living there, there are some over tax breaks. You can also get tax breaks on employing people.
Berlin is cheap, but hiring people is expensive, but there are loads of start ups there. German Tax laws account for 2/3rd of all tax laws in the world. Somewhere there are tax incentives for R&D investment.
For corporate structure you should look at using a Irish company, as this is far simpler than starting a company in the Netherlands or Germany.
Amsterdam would be a very nice choice in many ways, and living in the country to save on costs would be a reasonable compromise.
Their residency permit requirements are reasonable as well.
I didn't think of Berlin as being cheap. Will have to look into that. Berlin is very appealing for a number of reasons as well.