New top - would you do plastic or glass window?

[Deserion]

Personally I'd stick with plastic if that's what the roof came with originally. Overall I prefer the look of the 2003+ glass roofs over the ones like the GAHH roof since the window is larger (and the roof designed for it).

Use of the glass tops on the 1997-2002 frames is really personal preference, some like it and some don't. You could retrofit the 2003-2004 roof on there instead (which is what I would do if going from plastic to glass).

[Kiritsugu]

Glass, because it reacts more kindly to repeated temperature change and is stronger. Though Plastic is lighter, if you're trying to shed every last milligram for some reason.