That's not even a mechanical difference, the additive nature of the two is still the same. The biggest mechanical difference is Threes moves tiles one space at a time, while 2048 moves tiles as far as they can go.
You're right, of course -- though the 1&2 vs. 2&4 is still a mechanical difference due to the random distribution of the new tiles. In Threes, you can be faced with a long string of 1s without seeing any 2s (and vice-versa); such a problem doesn't exist in 2048, since you can match the tiles with themselves.