Yes, the BOSS GT-6 is better than the MT-2.

One thing that you just reminded me of, Azrael, is one pet peeve that I had with the GT-6. There's no completely clean channel. You can't have a pure signal travelling from your guitar to the GT-6 to your amp without it getting processed somehow, whether it's chorus, delay, compression, etc.

I think that's one of the main reasons (along with cost and simplicity to use) that I went with bunch of pedals instead of the GT-6.