As others have stated, MATX motherboards are more than enough for at least 90% of the users out there. Their computing needs are very basic after all. It is only the enthusiast that are feeling a bit cramped.
The fault lies not with the ATX standard but rather with the need for legacy PCI support. This is compounded by the large dual slot HSF's on today's top end video cards. Get rid of all but one PCI slot (just for those few legacy parts), put in PCI-E slots in the rest of the motherboard and this will open up room for PCI-E add-on boards.
One of the problems is that a lot of stuff still hasn't moved to PCI-E since PCI still provides enough bandwidth for the intended applications of these add-on boards. Vendors would be putting money towards moving to PCI-E when PCI is still alive and well. Compounding the problem is the lack of available PCI-E slots on motherboards...which leads to add-on vendors not supporting PCI-E yet...which leads to lack of PCI-E slots on motherboards...etc. It's the chicken and the egg scenario.
PCI-E will get there eventually but for now, we have the current situation where we need legacy support for PCI while trying to move to an all PCI-E system. It's much like how PS2 keyboards and mice are still around, and thus PS2 ports are on motherboards, when USB has been around for so long.