He's always been that big compared to Mew. Even in the anime movie, he's the size of a large human, whereas Mew is about the size of a small cat. The 'Dex entries say that height measurement is pretty accurate, too. Mewtwo measures about 6'7", and Mew is 1'4".
I mean, he is a genetically engineered clone of Mew, not the direct offspring. His DNA was horribly spliced and tampered with, so his much larger size probably has everything to do with that.