The compartmentalized stories of Ezio and Altair are fine (pretty hokey to be honest, but interesting enough), but the freakin present day stuff with Desmond and the "conspiracy" that's been shoehorned into it is one of the most convoluted things out there. A lot of people defend it by saying "we don't know everything yet, it's a big mystery we're unraveling!!!" and that's all fine and good, but it's pretty clear even the writers don't know what they're doing or where they're even going with it.