If I were faced with the same decision, I would choose the RX-V2400. Being a current receiver with all the latest decoding formats, it would be a better deal than the older model.
There are no discrete 6.1 or 7.1 DVDs in existence (DTS-ES 6.1 isn't fully discrete because the 6th channel is also matrixed into the side surround channels). However, PLII can convert 2 channels to 5.1. PLIIx can convert 2 channels or 5.1 channels into either 6.1 or 7.1. PLII and PLIIx have Movie, Music and Game modes as well. PLII(x) Music is highly configurable and I use it for everything, including normal cable television channels. I don't know how old the 3000 is, but I bet it doesn't support these new decoding formats (definitely NOT PLIIx as that is very new).
If you don't need or want 7.1, you can always use the two surround backs to drive a stereo pair of speakers in zone2 - say the Patio.