In the past they were not considered bioequivalent because of the lack of direct bioequivalency comparison studies to support the statement of bioequivalence. It's not so much that one brand is distinguished from another by any advantages or disadvantages, but rather that when a physician started a patient on a dose of a medication and titrates them up to a "stable" dose, switching it to another brand could cause them to receive a different amount of thyroid hormone and put them into hypo/hyperthyroid states.
As for why there are so many different brands, I'm sure I don't have the entire story, but each company could make money as long as physicians wrote for the thyroid hormone that they produce, since pharmacists couldn't substitute it with another brand - this isn't necessarily bad, since having multiple brands available ensures that there is some degree of competition and that no one company holds a monopoly on thyroid hormone. However, it does make it difficult for pharmacists and physicians to help their patients by trying to convert to a cheaper brand or something that's available.
Generic levotyhroxine exists - before, they were only be considered bioequivalent to specific brands (the generic companies produced the bioequivalency studies in order to get approval for the generic - I guess there weren't these studies comparing the brands to each other)...so you couldn't substitute Synthroid 100mcg with Mylan generic levothyroxine 100mcg for example, but you could substitute Mylan generic levothyroxine for Unithroid.
Looks like at least for levothyroxine, several products are considered therapeutically equivalent now, per the FDA:
http://www.fda.gov/downloads/Drugs/...ormationforPatientsandProviders/UCM186430.pdf
So seems you can substitute Synthroid, Levoxyl, and Unithroid with the Mylan generic now, though it looks like you can't switch between Synthroid and Levoxyl (see page 11 Beioequivalence studies).