It depends what you want overall. For a bike in the long term, go with the Ninja 300. The larger displacement and extra cylinder will keep you entertained for much longer, and fit better as an all-around bike.
The CBR250R is great too; very nimble and lightweight. Also torquey too and easily controlled.
Each, if you choose to resell, hold their value quite well. But most people who have sold them (especially the Ninja 250R) miss them a lot.
However i tend to have a sight bias for the green machines.
Maybe i was some kind of help if any.
Cheers and happy riding.
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