Final answer: as much as I'd like to account for the Oracle being missing by having her assimilated earlier (which allows a smoother transition later from her chip/message to the Merovigian visit), I still feel Seraph has to introduce the concept of the backdoors, and Neo needs to fight the plural Smiths as a setup to what's to come in M3. I'm sad, but it makes the rest work better.
I'm just trimming so she is no longer in hiding, they just weren't looking for her until she sends a chip that she wants to meet.
Which means if someone else wants to use that for their own edit, I give my blessing. I'd rather see all possible ideas explored then being petty over whose idea is whose.