Leaving the CPU off the motherboard makes sense to me. If he put one on, it wouldn't be cheap and it wouldn't satisfy every customer. People that want this board are likely to want something better than a 14Mhz 020 but with 680x0 series chip supplies being harder to source and FPGA accelerator boards out performing the real thing, designing in a specific 680x0 chip on the motherboard could be unwise.
No external floppy drive connector, no big deal. Floppy drives are outdated and you don't need two of them on a new Amiga design, one internal option is enough. The removable CF card provides extra file transfer/storage options as do the optional USB and network add-ons. Leaving out the external floppy connector I assume makes space for a VGA connector at the back of an A500.
The black & white only composite output sounds a little odd. I assume it's to discourage it's use. If a cheap colour option had been included instead that "poor" quality output may have ended up being used long term by people that don't get around to trying something better. This way you are forced to get a quality video output option.
Since the PCMCIA port is not include, which makes sense as it is an outdated technology that got replaced by USB ports and integration of wifi/network adapters, more memory, optical drives, flash memory etc in the PC world. I'd like to see USB included as standard on the new motherboard.
Using a modern laptop power supply makes sense. It can be cheap and will do the job reliably compared to old Amiga PSU's.
Keyboard options are bound to be limited to re-using an old A500 or A1200 keyboard given the target housings unless somebody hacks together or sources an alternative new keyboard solution.
The legacy parallel, serial and joystick ports are all very cheap to include as you've got the full chipset and these standard connectors cost peanuts. So although the parallel and serial ports may not see much action these days there inclusion seems reasonalbe. A modern mouse port (PS2 or USB) with a (microcontroller if needed and) jumper to translate the mouse signals to the Amiga mouse input would make a good addition. Amiga mice are hard to find, don't or wont last forever and aren't generally the best ever designs.
I'd like to see a real time clock included as standard on the motherboard. When most A500s and A1200s were sold as floppy only machines leaving a clock (and leaky battery) off the motherboard saving a few cents on the BOM probably made some sense but what motherboard doesn't include an RTC in this day and age. Just don't choose a leaky old battery type like they did back in the day.
Leaving the network adapter off the motherboard probably makes sense if it keeps the initial cost down significantly. Only machines with a fast CPU and plenty of memory can run a web browser to any usable degree and people aren't short of devices for tasks like e-mails, irc and web browsing. Any smart phone or tablet will outperform a classic amiga for these.