I own the RX-A3000. The HQV upscaler does do a good job, but you must feed it a signal that conforms to standards or else it does some...weird things (DirecTV SD receivers cannot be upscaled without the video shifting by a good 30 pixels or more because of this). I suggest not using the noise reduction feature if you can avoid it, as it doesn't really do much for console video, even analog.
Your best bet is to set the upscaler to 1080p or whatever your maximum resolution is on the plasma TV and make sure that
only that input is using the upscaler. Also, be aware that if you use this feature that you may also end up with input lag, so you may need to fiddle with the Lip Sync function at the same time to "line up" your inputs vs. the video display. Once you have this set up, you should assign
both functions to a SCENE button. If you are already using SCENE 1-4, you can assign them to SCENE 5-12, but be aware that those can only be accessed via the onscreen menus or via discrete codes via a Harmony remote from Logitech. You will then need to set up a second SCENE button with Lip Sync set to "0", as well as the HQV upscaler set to "Through".
Note: If your TV supports ARC (audio return channel) and/or auto-lip sync, you may not need to mess with the Lip Sync setting as this AVR also supports automatic adjustment of that feature as long as the TV also does.
BTW you do
not have to bind an input to a SCENE button. You can simply deactivate all settings you aren't using, activate the ones you want, and then assign that and that only to a SCENE button. I do this for my Lip Sync (0/120ms) since I frequently use Game Mode for my games which requires Lip Sync off, and my TV's motion smoothing mode which introduces 120ms of input lag, thus requiring audio re-sync. I also have two dedicated SCENE buttons for small and large speaker settings, in case I want to watch a movie and it's later in the evening where I can't use my Polk MicroPro 4000 sub (it can knock the drinks off the tables downstairs from my room upstairs).
Once you have your AVR set up properly, if you have a computer nearby that can run Windows, you might want to download
Receiver Manager, which lets you set all of this up via a Windows GUI instead of having to navigate the AVR's god awful menu system. You can save, back up, and restore settings instantly via Receiver Manager, so it is well worth the effort to learn its UI and put it to good use. Just make sure you give your AVR an IP address and proper subnet mask on your LAN so you can access it before you launch Receiver Manager.