Colonization is one of the best/most complete games ever made. I look at it as a very complex board game that would be very hard to play without the help of a computer. So the idea of a remake, taking advantage of the open source age, has a lot of potential: improved pixel graphics, improved mechanics and strategy (e.g. Slavery - since the game already mentions the instrumentalization of criminals and natives during colonization there is no reason to not mention slavery. It's part of our History and you cannot erase it. Censuring this is distopic).
By the other hand - to facilitate contributions - using Java is not optimal but it certainly made sense at the time, this is already an old project.
I patched FreeCol multiplayer in 2014. I was not a Java developer. But it was instrumental to how easy it was to fix this tricky bug in an hour.
On the contrary many open source games use Java (or CSharp) and it helps them be moddable, discoverable and testable in ways that JavaScript would not give you for free. Additionally, the web ecosystem is built around a marketplace of external services and opaque, bundled offerings, which makes people not paying those bills (ie modders, open source contributors) second class citizens in the development process.
By the other hand - to facilitate contributions - using Java is not optimal but it certainly made sense at the time, this is already an old project.