A stronger British presence in the East Indies? Welp. My first thought is that suddenly the Philippines becomes much richer. Why you ask? They are perfectly placed to be the heart of a British East Asia policy.
Whilst I can't see the immediate effect (perhaps more influence in Japan and China?) I think the biggest impact would be a change in policy during the Napoleonic Wars, butterflies permitting. I think Britain would spare resources to annex all Napoleonic Dutch territory in the region - using the Philippines as their stronghold for naval activities.
Or at least, that is my first instinct. What is terrifying about this is, apart from the near complete ownership of the spice trade, is how much stronger that would make the British. Fiscally, they don't have as immediate a fiscal problem, meaning we might avoid an alt-Opium war, but Britain now has India, AND Indonesia. Say goodbye to an independent Indochina as you see Indonesian Sepoy armies being raised.
The scary thing is, if Britain STILL needs an Opium War, with the manpower and logistics hub in the Philippines and Indonesia, and the resources of India - Britain could legitimately have a chance of conquering swathes of China and holding it if they needed to (I can't see why, besides an obstinate Chinese Emperor refusing to trade). Indonesians/Indians taking the role of the occupying forces, but that depends on if Britain wants to forcibly tear open a market, rather than simply force it open.
As much as this makes the British Empire more of an East Asian Empire, I think this could prevent a number of European Wars. Britain would be capable of deploying to any part of Russia, any colonial territory, and potentially bring in huge numbers of Sepoy-style troops. Japan has little hope of anything but being a satellite to Britain, because if Britain sees China as part of their East Asian sphere, a Japanese invasion will be seen as an affront.
I'd kind of hope that the increased wealth from owning Indonesia might lead to food subsidies for Ireland and India during their famines, but I'm not exactly sold that it'd happen. But what might happen, even if it is just from lunging for Indonesia, is a realisation that the British Empires "Ship it all home and back out to the colonies" model of Empire isn't going to work, as smuggling to partake in standard trade between India, Indonesia and China will be so expensive to stop, that it might as well be legalised. If that then becomes legal, Britain will be getting some sort of fees coming home, on a scale that is large enough to reconsider their plans.