The TPS6xxxx series is a switching regulator. Have you followed the datasheets directions on selecting proper components and PCB layout? They are (relatively) tricky to get right.
No 22pf (x2) and 1M resistor around the crystal? (or are you using a resonator instead?) Is R4/R5 value too low? (don't know what kind of LED you're using)Does it need to be a switching regulator? What's the power source? Can't you just use an LDO (Low Drop Out) linear regulator?No bypass 0.1uf caps for U1, GPS module, U2, etc (Vcc pins)... You need those (just to be safe/proper.) I'd probably add one in parallel with C1 too. Might as well add a pull up resistor from Mega-pin10 to Vcc (in conjunction with SW1). Junction in your schematic missing (from P$2 of resonator to GND line). (When you design your board, the pcb layout module wouldn't know something is amiss.)
Just a general suggestion: use net names so you don't have to physically drag wires to connect D3 to wakeup. Instead, you add a wire to the pin D3 and name that wire net "D3". Add a wire to wakeup and name it "D3". It's much more readable than tracing green wires with my eyes.
Thanks! Is that how you make the little square arrow with the name of the connection that it goes to inside of it?