I would recommend no ground plane / copper pour around the converter. It isn't needed, adds unhelpful parasitic capacitance, and can lead to lots of switching hash entering your ground and possibly causing problems with the rest of your circuit. The extra trace inductance should be negligible in a boost converter as long as you provide a reasonable return path from the ground side of the switch back to your input cap. It might make radiated EMI slightly worse, but the main source of EMI from a SMPS is magnetic fields from the inductor which is not shielded at all by a copper pour. As long as your device goes in a metal enclosure you will be fine.
Keep all the switch-mode converter stuff in its own section of the PCB separated from the digital circuitry. If the converter is really noisy, you may have to replace the output capacitor with a capacitor-inductor-capacitor "pi" filter where the supply goes to the MCU section. On the MCU side you ideally want a 4-layer board with complete power and ground planes on the inside and signals on the outside. Failing that, try a complete ground plane on the bottom and all your traces on the top. Unfortunately, this is rarely possible for digital applications. Almost always at least a few traces need to cross, and you can't do that without cutting into your ground plane -- at which point it is not really a ground plane any more. What to do then depends on your speed, your noise immunity requirements, and what EMC requirements you have to meet. Options include wire links to jumper traces, getting rid of the ground plane and using a ground pour in unused space, close your eyes and pay for 4 layers, or abandoning the project. Jumper wires deserve special mention: they are usually considered unacceptable in a production product, but it is perfectly acceptable to have a few in a prototype or one-off, especially if you know you are willing to pay for 4 layers when you go to production.