It depends on what you are wanting from the unit. Very possibly, you will want some of the newer HDMI version features that the RX-V3900 does not support. It is HDMI version 1.3a (see
this) which can be compared with newer versions
here.
If you are discussing the RX-A2010, it is about the same level of receiver, only newer by a few years, so the HDMI that it has is capable of more things (see links above; also compare
this and
this). It also has more HDMI inputs, which may also matter to you.
If the RX-A2010 is new (though it, too, is a discontinued model now) and the RX-V3900 is used, then it is more than worth the extra $250. But it is possible that you don't need any of the newer features, and the RX-V3900 might be all you need. And if it is all you need, then spending more is unnecessary. I currently use an even older RX-V2700, and I do not intend to upgrade any time soon, as it does all that I currently need from it.
Without knowing exactly what you are wanting to do, it is impossible to say whether you need any of the newer features or not. But I think most people would be better off buying the newer unit, as it does more of what people are more likely to want these days. It is the one I would select from those two with a $250 price difference, even if both are new in factory sealed boxes. If they are both used, then condition comes into play, but with nearly equal condition, I would buy the newer one, the RX-A2010.