Taiwan instead of the Philippines

Would the United States have been better off taking Taiwan rather than the Philippines?

It would be strategically consequential, but it requires a radically different earlier war and likely worsens relations with Japan.

Taiwan was not part of the Spanish-American settlement, so acquiring it would require a different war rather than a different choice from the same peace terms. An American-held island so close to Japan would create a major strategic rivalry much earlier than the historical Pacific confrontation. One possible consequence is an American-Japanese war replacing the Russo-Japanese War around 1905. The international system and both navies were very different then, which prevents a simple verdict on whether Taiwan was a better possession than the Philippines.