Strange PCB software as I don't see any pads for the 40 pin device on the underside of the board.
Anyway, a few things to think about.
Power rails are too thin. You really want to try and use heavier tracks for carrying power. On 2 layer designs and depending on the needs of the devices, I run 40 or 60 mil power rails for both GROUND and VCC (3.3, 5.0 etc)
Add a decoupling cap (0.1uF) next to U1
I can't see any tracks from from one side of L1. Keep these are short as possible and heavier (same as the power rails) between the inductor and the MCP16301.
I assume this is for a motorbike so there is no radio to worry about causing interference to. If so you need to add a filter on the input as the power rails could potentially generate a lot of EMC. Murata do some very nice automotive spec inlet filters for this purpose. Using a spectrum analyser and some EMC test kit I saw a huge drop in the transmitted signals on the power rails. All my designs now include these
What is the reason for the 10K pull up and 10K pull down on the ENC inputs? With no signal on these, the voltage on the input will be around 1.65V. Is there a reason for this? You really only need one of the other depending on how the encoder works.