The reason I'll recommend brotherhood over 2003 to start with is simply because that's what you'll likely discuss with people when you want to talk about fullmetal alchemist, that's what most know and love.
This might be true with younger anime fans, but I don't think it's true in general.
The original FMA was massive. It was one of the most popular anime of all time in the US, airing on television when anime was basically at the peak of the anime boom, receiving numerous re-releases on home video with each version selling well, etc. Brotherhood came along many years later when the market was significantly weaker, so even though it aired on TV, it was seen by a smaller number of people.
The 2003 series was legitimately on the same level as shows like Cowboy Bebop and Yu Yu Hakusho in terms of how well known and liked it was from general anime fans at the time. Brotherhood has never reached that level of popularity.
I never said they shouldn't have done it. My point is as it stands now in 2016 and not 2003, the manga is ended and he has both options available.
The original is fine like I said, and it does explore parts that Brotherhood doesn't. But the important canonical stuff and the ending is all in Brotherhood anyway. Animation is much better too. If he has both options, why not go with that one? Chances are he won't watch Brotherhood once he watches the original, and will move on to something else. He's getting started on watching anime. So let's have him watch the conclusive version instead. Does that make sense?
The animation is better in the 2003 version, not in Brotherhood.
And being "canonical" doesn't mean anything. It's a different story. I would say a better story.
As far as I'm concerned, there really isn't a single thing Brotherhood does better, or even as good, as the original version.