Warning: Some mild spoilers:

I think the special effects people took note of how awful the effects were in 'Reloaded' and decided to "cheat" with the effects on Revolutions. Having the final fight scene in the rain and at night would cover up the fact that their computer generated Neo & Agent Smith aren't very good (the movie Godzilla awhile back also used this cheat.)Also, the fact that they had the rest of the Agent Smiths "just watch" shows that as well.....I thought the ending though was a bit of an unhappy ending....