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I did that train ride a few years ago and remember sitting on the right side of the train. The River was on the right side for most of the time as well.
We were in a compartment and we could always go outside to stand in the corridor to look out on the left side as well. I don't remember it being a very narrow valley, so I think you have some views on both sides.
Also I don't think the whole two and a half hours were super special.
Edit: I just realized you are going from Zagreb to Ljubljana, I went the other way, so in that case sit on the left side of the train.