Out of all my playtime as Malacca, the 17th century was by far the most eventful, but my updates come slowly enough as it is so I’m just going to hit the highlights and then get with the screenshots.
The first third of the century was pretty tame. Some growth, some colonization. I became good friends with the one-province sultanate of Brunei and later made them into a vassal state. Vassals in EU2 give half their income to their parent state, but stay basically autonomous. The relationship can be formed through diplomacy, as happened with Brunei, or through conquest. An example of the second kind is the Hindu state of Mataram, which I was fighting around this time, and which I eventually defeated and forced into vassalage. Later, I discovered that while vassals may not attack their parent states without severe penalties, they are perfectly free to fight each other, and I enjoyed great entertainment from the Brunei-Mataram wars that would occasionally erupt as I went about colonizing the rest of the archipelago.
For Malacca, the turning point came in the late 1620s with the appearance of its greatest ruler, Abd Jalil Shah II. A mighty leader and a formidable army commander (some rulers in EU2 can lead armies in the field), he governed for nearly half a century. Under his leadership, the Malacca Sultanate expanded its territory by both colony and conquest, and grew from a modest kingdom into a bona fide empire.
The first great victory was the unification of Sumatra. In 1643, I took advantage of our Royal Marriage with Atjeh to claim their throne, followed by a declaration of war. The Shah led his armies across the Strait of Malacca and oversaw a speedy campaign. By 1644, Atjeh was subdued, and I took the province of Riau for myself and forced the rest of Atjeh into vassal status. That arrangement only lasted three decades. In 1667, perhaps in a form of suicide by proxy, Atjeh declared war on Ayutthaya, who promptly conquered and annexed it. That seemed as good an excuse as any for me to step in, so Malacca immediately went to war with her Siamese neighbor. In 1669 Ayutthaya ceded the provence of Atjeh, and Sumatra was finally united under Malaccan control.
Around this time I began negotiating exchanges of map information with friendly Sunni states in the Near East, such as the Ottoman and Mughal empires, and through them Malacca finally became aware of Europe.
On the mainland, in 1655, we seized the province of Phuket from Ayutthaya. In 1689, thankfully, it converted from Buddhism to Islam, making the populace far more manageable. That was, by choice, my only gain in mainland territory throughout the game. But it was enough — Ayutthaya was never a significant threat to Malacca after that.
Abd Jalil Shah II died in 1677. He was replaced by the much less impressive Ibrahim Shah, who was replaced in 1685 by the even less impressive Mahmud Shah, and so on for the rest of history. From this point, it would be the colonists and traders who would write the remainder of Malaccan history.
An interesting thing happened in the 1670s. China — as though it had nothing better to do in the midst of its endless war with the Manchu — began to sail a force around Indonesia, massacring natives on every empty island it could find. Why it did this I can’t say. I suspect China was clearing the way for future colonization efforts which it never got around to. I wasn’t pleased by all this slaughter — it denied me untold thousands of potential Malaccan citizens — but I decided to take the opportunity to colonize these now much safer provinces before China or anyone else could. So in 1683, we finally established a colony on Bandung in central Java, its hostile natives having been erased by the meddling Chinese in the previous decade.
Finally, in November 1688, the Colonial Dynamism random event happened. Malacca received its first conquistador, one Colonel Hamzah, giving me the long-awaited power to explore unknown land zones. Although exploring sea zones require a different kind of unit, there were lots of islands in the places I already knew about which could be explored. In April 1689 Hamzah began his first voyage, to Palawan, which turned out to be home to angry natives and a great deal of fish. Over the next decade he visited the remainder of the Spice Islands, discovered the Phillipines (still untouched by European feet), and even sailed as far as Taiwan. Malacca established a colony on Taiwan in 1695, just to remind China who this ocean belonged to.
Hamzah died in November 1700, and that brings an end to this chapter of Malaccan history. At this point the East Indies look like this:

Bonus: The Indian subcontinent.

Heady days for the Ottoman Empire.