As far as I know there is no official explanation, but the most likely reason is to balance the game. As Evolutionary Stones can be found fairly early in the game which means the player can get final evolution's just as early, and thus a balance mechanic was implemented to prevent them from breaking the game. By having them learn few to no viable moves the player is incentived to wait evolving them until they have learnt better moves. By having this trade off the gameplay becomes more varied in that there are options, that you get more control of what your teams will look like and the games become more balanced.
An example of this would be the Nidoran family in R/S/Y and FR/LG. Nidoran can be obtained before the first gym, and Moon Stones can be obtained at Mt Moon, before the first gym. This means you could have a Nidoking/Nidoqueen before fighting the second gym. Had the Nidos not had such garbage movepools the Nidos would allow anyone to steamroll the entire game with little to no grinding.
So in short, its a balancing measure, preventing Pokemon that evolve with Stones from breaking the games.