I understand your dilemma, most of us have been in the same position. Based on what I know now, IMHO, I would dedicate a decent amount to your left, center and right speakers. This is where the quality needs to be given that your critical sound will be produced from them. The surrounds can be less expensive, but I would keep them in the same family as your mains (but not totally required). The subwoofer does not need to be timber matched to your speakers. One thing I have learned over the years is that your speakers will be around a lot longer than your current AVR (case in point - you just bought one 3 years ago). My first real AVR had dolby 5.0 surround, I later upgraded to a dolby digital 7.1 and then again to an AVR with HDMI inputs - 1st generation 3D came out the next year (pretty sure there will be a next generation 3D at some point or more wifi capabilities)
Regarding the use of 7, 9 or 11 speakers - that is up to you. Nice to think about anyway (I'm wired for 9.2, but only use 7.1 at the moment). The majority of content out there is coded at 5.1 and the AVR processor fills in the other channels electronically.
Using 7.1 is great and I really enjoy it, but it only really works well if there is some distance (at least 4') between the speaker and the listener. For example: using rear surrounds - If your seating is along a back wall and you have rear speakers behind or next to your head - they will be too distracting.
Pre outs: You would use a "pre out" if you were looking to bypass the AVR amplifier and power certain speakers with a separate amplifier. For example: AVR - connected by RCA cables to Amplifier which in turn has a speaker or speakers wired to the Amp
FYI - I have the TX-NR3007 mostly because I needed the extra HDMI inputs, multiple zones, 7.1 and decent power.