First one I played was Brotherhood, and I loved it, I hadnt played anything like it before (and I loved that Danny Wallace was one of the voices) It was certainly a close conteder for a favourite of the series.
I did also really enjoy Syndicate, mainly because I lived in London at the time and I could free run along the street I lived on, so many times I dreamt of actually running along my rooftop.
My all time favourite though was Unity, I replayed it (admitedly when it was free) after the fire at Notre Dame, The scenery was amazing, The Notre Dame Cathederal was breathtaking and giving the game away free to raise the awareness of it was an amazing thing to do, thats what made it my clear favourite.