Without seeing schematic just a few thoughts -
1) Pads for 32 Khz xtal and caps (2) needed.
2) A gnd pin strip/buss on one edge of board for connecting scope probe ground and other
3) Split analog and digital grounds, then join at common point. Pads in analog ground
path for SMT inductor, or SMT short, and jumper pins across pads, and two sets of pads
each side of SMT L for ceramic and tanatlum/electrolytic. Would not hurt to do same
on digital side.
4) Thru holes for a piezo buzzer of some sort.
5) Jumpers to allow battery operation or regulated supply.
6) A few SMT LED pads with corresponding current limiting R pads and jumpers to connect to pins.
7) Pads in main power line downstream regulator to take SMT R for use in making current drain measurements.
Eight pin port header to take LCD display. Oriented so display when plugged in not over board,
and oriented so display can be read along with solder mask pin labels on board, eg. nothing
winds up upside down.
9) Pads for a few P-B switches, say 4 minimum, with pads for pullups and jumpers to pins.
10) Pads for a 3 pin temp sensor with jumpers to select analog pin to drive. Same for accelerometer
and pressure and light.
11) A PCB proto area, PCB area is cheap.
Note SMT could be thru hole solutions/layout, make it easier to proto.
Look at schematics of other boards for additional ideas.