hmm I initially thought you meant they should have ported the C Quake 3 engine to Java (which wouldn’t make much sense), but now I see why it could have made sense to use the java plugin (and probably still does for the Mac and Linux ports).
All they’d have to do was launch the c version of Quake 3, grab its window handle and stick it on the applet.
which would leave the problem of javascript communicating with the quake engine, which could probably be done with some jni.
They’d have to make java plugin 2 a requirement though if they’d want any form of stability.
looking at the horrid state of applets when they started the project, i don’t blame them for going the custom plugin way.