They are virtually the same but the Thunder has less features (Reverb, less switchable options etc). I don't think there is a big sound difference.
Other combos I would recommend are the Marshall VM series (the 2 channel ones, price wise). If you also want classic rock tones and not just modern scooped buzzbees, I would prefer those. Less versatile but great sounding would be a Rockerverb 50 from Orange, or even a Rocker 30 (sounds great). But they have an Orange character, so they are more Pearl Jam than Metallica.