Question: Does anyone have a clue why Anakin Skywalker from The Phantom Menace was given a normal sized body instead of a shorter one like other smaller characters in the game?
Answer: Because they are Lego. Most Lego men regardless of age or species are the exact same size.
Characters who are significantly smaller/shorter (typically young children) are usually depicted with shorter legs in Lego games, those type of legs which aren't rotatable and doesn't have holes in them (excluding the bottom of their feet). Yoda and Boba Fett (From Attack of the Clones), on the other hand, has those type of legs in the game.
At the time of Phantom Menace, Lego did not have those short legs. By the time Attack of the Clones was released, they had developed them. The use of long legs for Anakin is accurate.
Answer: Originally they were not. The earliest Lego Star Wars sets had normal sized legs.