here is how I decide how to play them. This assumes I have every game in the series.
If they span MORE than 2 console generations then I play them in order of release dates so that It doesn't ruin my enjoyment of the series if the first released is lacking a lot of features of more current games in the series.
If they do not span more than 2 console generations IE started on ps3, 360, wii, till current gen or it started on NES and ended on SNES then I play them chronologically.
of course its easier in theory than in practice because I will get a few from the series and just play through it all anyway. like not having .hack infecton but having beat mutation, outbreak and quarintine