You mean they sent you the MX5500 free after a bit of nagging? Interesting. I would rather be stuck with an intermittent mx3100 than a mx3200 tbh, my housemate has one and i find the whole thing really lacking the quality of normal logitech kit. The mouse is unresponsive (and not rechargeable), the keyboard isn't as cushioned as mine either.
My argument would simply be, the MX3100 was the top offering from logitech when I purchased it, and it set me back £80, I want the top (equivalent) model again.
No nagging at all to be honest, I just asked if the MX5500 was available and they said they'd send me it. Did mean waiting a while for it to be released, but the fact they were happy to let me do that (rather than just send me whatever and get rid of me) shows how good they are.
Your argument should be valid though, the MX3100 was indeed the best keyboard + mouse set available when I bought it, so the MX5500 is a fair replacement. Been very happy with mine.
Varsh: I highly doubt you'll be able to get another MX1000, they stopped making them a while ago I believe. The MX Revolution is probably the most appropriate replacement, I went from an MX1000 to an MX Revolution (as above) though, and it's been fine.