The most noticeable difference is that VST3 allows side chaining, so if you own plugins that support it (most often compressors and gates, Waves RComp for instance) you'll want to use the VST3 versions. Otherwise I don't think there's a difference. Caveat with Waves specifically is that you can't mix VST2 and 3 ones within the same session. So pick one and stick with it, you can have Sonar automatically "hide related VST2 plugins" which helps with that.