in EXE megaman was just data, the cross fusion they did kinda made him human, added a little real life touch to it, in starforce as you can see they went straight for the synchronization idea, so dont think its branching off that much, remember this time its EM waves, still electronic hence the electro in electromagnetic. Getting away from the original idea of being a robot is essential if they want to make another series off the timeline, if they didn't it would be repetitive and hence the idea would not be original and may lead to lack of sales.
To compare off the top of my head Square Enix or rather Square Soft in the past has always had the protagonist end up with the hot black haired chick (who for some reason always looks the same) in all the final fantasy games that had decent storylines (later ones that didnt consist of your party farming magical gems/crystals/other magical rocks).
No need for capcom to break tradition either ^.^