Hey MagicVinny
Ok firstly lets consider the 3009 (firstly I am guessing you know its a receiver and not just a pre amp?) - Will you be using a power amp along side this (using the pre-outs on the 3009) or just the AVR as it is? I think the only real difference with the 3009 compared to the previous series 3008/5008 will be the addition of the 4K upscaling and upgraded network features but since you won't be using the video options and placing the video straight to the screen you don't need to worry about that. So maybe an older AVR could be worthwhile - I used to have the 3008 before upgrading to the 5508, while it sounded great with my B&W 600 series - it didn't have enough power to drive the 800 series.
Now talking about the 5507 - yes it is a great processor, however will you be wanting any Room EQ ? I only ask since the 5507 only has the Audyessy XT eq, and not the XT32 (higher resolution filters applied to signal), to allow for increased detailed equalisation. There are a couple of people on here than have upgraded their AVRs and Pre/pros for such technology - one chap is called i_raz - it may be worth asking him how he has found the upgrade. A great compromise to this would either be going for the 5508 if you could, or maybe another brand (unless you wanted to stick with Onkyo?).
Of course for my personal reasons as to the change from the AVR 3008 to the Pre/Pro 5508 - was not enough power from the Onkyo amps for my speaker setup, and too much power consumption from using both the AVR and Power amp together- since you cannot turn off the amps in the AVR while using the pre outs it was still consuming 1000watts + while just processing. I think overall I was using nearly 2.6Kw for just the sound which is way too much for my apartment (had trouble with fuses blowing).
Any how buddy - I hope that helps! If you need any more advice on the Onkyos give me a shout. I do think you would be best going down the seperates route - that way if you do need to upgrade the processing in future (this will be outdated before your power amp), you can do so more easily than if you were going down the AVR route.
Cheers
Phil.