Microcontroller and decoupling capacitors on the VDD layer
First of all, you don't have a VDD plane (What's VDDD? I'll call it VDD). You have a mixed signal plane.

There's absolutely no problem having the processor on the same side as the VDD copper. If it was, it would invalidate every two-layer PCB I have ever seen. Don't worry about that.

Since you have already made sure that all your current paths are laid out exactly as you want them, I see very little need filling the plane with VDD. From your initial layout, I suggest that you simply route your power traces back to the supply. This assuming you have a ground plane on the other side. Otherwise try to route the power traces close to the corresponding ground.