Full Metal Alchemist. This isn't even a contest.
Bleach and Naruto are entertaining, but exhibit many of the problems associated with animating long shonen action series. Like their pacing in general even before commercial realities like filler come into question.
Bones, with Square ENIX full support, made a brave decision to forge a new ending for an incomplete manga, and the result speaks for itself, the main strengths of the series are in its second half. As a result FMA has got excellent pacing and buildup, a superb ending and denouement. Its genuinely surprising and it perfectly illustrates the growth and developing maturity of the lead character, which is pretty much the central theme of these series.