I'd max out your best ones one at a time before working on the lower ones, dps is the most important thing for gyms and raids, and higher levels means more dps
However, with gen IV coming, you may want to invest more in Bite/Crunch sets, as theres a grand total of 5 legendary pokemon weak to dark, not to mention the already existent mewtwo EX raids, but 1 weak to rock (and that one is double weak to ice, and can super effect tyranitar, its sky shaymin, who may or may not even be added for a long time)
You may however want tohave enough saved up to max at least one SD in case rayquaza comes back if you dont have any sufficient ice or dragon types if the weather isnt partly cloudy often/wont be able to small group it