I read over on RetroRGB that the SNESjr had better RGB output than the original SNES, but that was never my experience. Turns out the RGB mod I designed when the system first came out was... sub optimal. ;)
Here's a comparison of RGB outputs, showing the GameSX SNESjr mod, the original SNES, the RetroRGB mod (http://retrorgb.com/snesminisrgb.html), and finally the RGB after running through an XRGB2. It's interesting that the capture from the XRGB is so good. I suspect the de-interlacing of the XCapture is involved here, my hunch is 240p is its weakness. The XRGB does a really great job with the upscaling, but I think maybe I've tweaked something at one point because the colour and brightness are a little off.
(http://nfggames.com/grafx/SNES-RGB-Variations.png)
The difference is the "add resistors to the RGB inputs that adjust the brightness" part? (1.2k resistors)