Timing depends on what you are looking for really:
Early-mid September is often best for American waders and seawatching, but chance of American passerines s best late Sept-October. Siberian/continental passerines etc. are usually thin on the ground if it's lows coming in off the Atlantic, but can get decent stuff if the weather does have an easterly component.
General wader migration is good right through though tailing off late Oct. As mentioned passerine migration (pipits and sky larks, wheatears aside) usually involves much smaller numbers than on the east coast.
Most raptors are still easily doable with reasonable weather in Autumn, sometimes easier than in spring ( SE owl disperse and become mainly nocturnal again so much harder than spring/summer). otter can be slightly easier too.
Ferry crossings especially in Sep can be good still for cetaceans/basking sharks. As for which ferry be aware that the Oban ferry is much more prone to delays/cancellations due to weather than the Uig crossing.
Weather potentially highly variable - you can get some nice settled spells, but equally you could get a run of Atlantic lows.
At the moment we still haven't got out of winter yet!!!