Looking at its location, it seems like it occupies a fairly important position along the old sea route to India. Yet it was only absorbed into France in 1897. The Portuguese also established bases in Mozambique, which is right across the water. Why was Madagascar ignored by colonial powers for so long?
We should make a distinction between trade and limited coastal settlements, and imperialist colonization in the Scramble for Africa style.
Portuguese reached Madagascar in 1500, almost immediately after Da Gama's first trip around the Cape of Good Hope. Between 1642 and 1674 French explorers established a series of settlements along the coast of Madagascar where they conducted trade, including trade in slaves.
Madagascar was home to several coastal settlements of European pirates in the 18th and early 19th centuries, as well as a source of slaves that made their way to the Cape Coast colony in southern africa.
In the first half of the 19th century, there were numerous English and French contacts with the expanding Merina kingdom. English missionaries were responsible for conversion of the kingdom to christianity, and establishing Malagasy as a written language.
At the same time, adventurers like Jean Laborde established sugar cane, clove, and tobacco plantations with the permission of the Merina kings and queens, as compensation for Laborde's role as Chief Engineer for the Merina monarchy and French envoy to Madagascar.
So, there was a fair amount of contact and trade between the peoples of Madagascar and Europeans for many centuries before France established a protectorate over Madagascar.
Secondly, 1897 is not actually that late in terms of the Scramble for Africa. Cecil Rhodes' British South Africa Company only established their rule over what is now Zimbabwe, Zambia and Malawi in 1890. The Fashoda Incident where columns of French and British troops faced in southern Sudan over competing claims to the region happened in 1898. Britain did not establish the Anglo-Egyptian Condominium in Sudan until 1899. British control over Northern Nigeria only happened in 1901.
So, the transition from European missionary and trade contact in the early 1800s to the Franco-Hova war and establishment of formal French protectorate in 1897 occurs in the same timeframe and has similar characteristics to other European countries interactions in Africa in the 19th century.