score:8
Japan was in fact vulnerable in the 16th century when the Portuguese and later the Spanish arrived.
But Japan had, despite the civil war, an educated and competent elite as well as an effective administration, aware of European technological advance and the potential danger of European colonization.
It was the activity of the Catholic missionaries and above all the attitude of the Franciscan religious and Spanish visitors in the early years of the 17th century, who were not so focused on the diplomacy and cultural understanding of the Jesuits and the Portuguese that determined the expulsion of all Europeans with the exception of the Dutch by various decrees between 1603 and 1639.
This period of isolation (Sakoku) lasted until 1868 during which time Dutch access was restricted to an annual visit to the island of Dejima in Nagasaki Bay. This period did not mean economic retrogression. Quite the contrary, the Japanese government kept itself informed of the world situation and technological advances through contacts with the Netherlands and invested in the development of its economy. Investment in education was very important.
When industrialization with Western technology began in 1868, Japan already had both capital and universal education and a population ready to take full advantage of industrialization.
Upvote:3
Besides the accepted answer's focus on obstacle of a complex society and (semi-)centralized government to a quick takeover, it probably wouldn't have been obviously worthwhile.
European colonization projects usually happened for one of two reasons:
Profits from resources. This would apply for example to most of Latin America and gold. Africa in the 19th century had ivory and rubber, at least in some instances. Parts of the Caribbean were colonized for salt.
Land takeover by European farmer colonies: Australia, North America, Algeria and South Africa.
Japan is not a resource rich country. Nor is it a particularly great area to do European style farming in, being already densely populated and mountainous. Rice is well-suited to it, wheat is not.
So, aside from other considerations, an extensive colonization project would have cost a lot, without obvious returns. Not great ROI prospects.