As for Matrix Reloaded...there were a few disappointing parts: you could see the animated frames; Trinity mounts a brand new motorbike (on the back of a lorry) and it has a full tank of petrol. I don't know if this is likely.
Good points...where Morpheus states: "what I believe doesn't require for others to believe for it to be true..." (ok it's not an accurate quote, but it'll do). Much was made of Neo's humanity. Also the statement that each has the same reason but a different purpose - I think the key maker says it.
Hopefully I haven't given much away to those who haven't seen it yet.