Yes, that’s what I said:
You should consider adding a 6 pin header, or at least pads, for an ICSP (In circuit Serial Progammer) so you can burn the bootloader into the ATmega32U4.
You should review all the decoupling capacitors in your schematic and consider their values and whether you need more or less. For instance, you probably don’t need all of C3, C7 and C11. You may want to increase the size of C9 and C10 to 1uF or higher, as recommended in the AP7333 datasheet. You should add at least a 0.1uF decoupling capacitor close to the ATmega32U4 power pins and probably one for the display and one for the flash chip, as well.
When you removed the level shifter, I’m not sure if you joined up the traces properly When I try to highlight connections to the flash chip, I don’t always see the full path. You may have this problem in other places, as well. (Or maybe that;'s just how EasyEDA works.)
Depending on the mAh rating of the LiPo battery that you use, you may need to adjust the value of R10. The 2K resistor used by the Arduboy is actually too low. It will give a charge current of 500mA. For most small LiPo batteries the recommended charge current is 1C. For the Arduboy’s 180mAh battery that would be 180mA, so the 500mA charge rate is 2.7 times the recommended rate (which will reduce the life of the battery and maybe even cause it to overheat). The Arduboy should have used something closer to 6K.
If you think you might want to connect additional peripherals, and depending on the size and shape of your circuit board, you may wish to consider (or at least add pads for) a 12 pin expansion connector, as described by @Mr.Blinky. (Note that pin 8 has now been defined as connecting to A5).
You could also add pads for other unused I/O pins. The Arduboy circuit board has solder pads for almost all the useful pins, whether used internally or not.
Unless I missed something, everything else looks OK.