I love both shows for different reasons. Thunderbirds was much more 'emotional' (if such as thing can be said of a puppet show) than CS. It dragged a little but the Thunderbirds themselves were such cool looking aircraft that I could sit and watch them for hours as a kid. And the Tracy boys were suitably different enough to stick in the brain, and there were all those explosions.
Captain Scarlet was much darker, which made it a guilty pleasure. All those innocent people getting bumped off in the beginning and turned into the Mysterons! I have to admit, even as a kid, I found the premise of the Mysterons telling Spectrum when it was coming was a bit dense, but supercool, good looking secret agents battling aliens! Gotta love it.