Agreed, MtG is learned very fast, a great bonus point.
Commander is rather considered a casual mode. Modern and Standard are really big in MtG. Being competitive is what many MtG players strive for. So giving your opponent no chance to interact is often key. See control decks or Vintage format.
We have no Wrath of God, but we could create Wrath of Q
Its hard to catch up in STCCG when you get battled off the table. While in MtG you play best of 3 within 50 minutes, we often struggle to get 1 game of 2E in the same time. So if you get massacred game 1 in MtG, you still have the chance to win the other 2 games. In STCCG, when you get board whiped, you can only try to stop your opponent from solving his missions. You are often too late to rebuild your crews/teams and you have only the one game. So in this perspective MtG offers hope. You can easily concede the first game, hoping the other 2 will not go south.
So the biggest disadvantage IMHO is that STCCG is sometimes more a board game rather than a fast paced card game. Unfortunately people want fast games and with that more (!!!) games during a tournament or in their hobby time.