As far as the actual ideas, I think that your explanation as to what happens to the oracle in the beginning is great. It didn't make much sense to me that the Oracle couldn't be found at the beginning of the movie. If she was assimilated or kidnapped that provides a much cooler opening.
The Seraph fight was okay, but it didn't add anything to the fight. To me, it was just filler. With the Oracle missing, it doesn't provide any purpose. Now, if you get a hold of footage in Enter the Matrix, there is another Seraph fight between Seraph and Niobe. If you really want to see Seraph fight, maybe you could use that footage instead.
I never liked the Smith fight in the park. The extra copies of Agent Smith coming from eveywhere was the only part I thought looked cool. The rest of it, especially when they have Neo fighting with the pole and using it to spin around and kick all the Smiths which was a particularly bad (bad cgi=fake looking) effects shot, was just cheesy and drawn out. I would not miss if you cut it.
I don't understand how you would make the Smith fight work at the beginning of the movie, but I'd be interested in seeing how you accomplish it. The final battle is supposed to be the culmination of two films worth of build-up. It is the moment everyone is waiting for in the official films. It is just a great moment in cinematography. Much better than the battle in the park by far, but than the fight in the park is supposed to be the fore-shadowing of the ultimate showdown. I guess you will have to make a decision on how you want to handle it. It's hard to comment on some of your ideas without knowing more about what you have in mind for the the sequels.