The original manga's creator, Hiromu Arakawa, requested the studio to deviate from the source material's plot about halfway through into the original 2003 anime So the first few episodes of FMA 2003 will be similar to Brotherhood but goes on to do its own thing later on. Brotherhood is through and through true to the source material manga.
I'd say FMA 2003 is worth a watch, but personally it doesn't hold a candle to Brotherhood. Animation, characters, the plot, and pretty much everything in it are so much better.