I tend to agree that a new baseline board with the essentials included would be preferable. The USB/VGA/NIC/CPU kludges we have now are driven by necessity to work with the classic motherboards.
Building these kludges into a new motherboard seems odd.
Who knows why this approach has been taken, it may be driven by I/O limitations of the AGA chips, build costs or a desire to shift a large stock of individual computers add on cards.
Whatever the reason, having new dedicated classic motherboards is a great thing, so hats off to Jens for sticking with it.