Lian Li cases are dang nice, but may or may not be the holy grail you're looking for. Unfortunately, I haven't found anything that is obviously better. Let me go down the list comparing it to the one I have (PC-65B). Most of the Lian Li cases are built roughly along the same lines, though I bought mine a year ago so there may be a few improvements (though the only major change I've heard of is the new budget case without a removeable motherboard tray).
Front ports: USB only on mine, but some of the newer ones come with firewire and audio in/out as well. Since it has 3 front accessable 3 1/2" drives, you might be able to add on a Firewire/audio in/out connector.
Removeable motherboard tray: Yup, and a nice one at that.
Pull out drives: removeable rack for 5 hard drives, right behind the two front intake fans (built in 3 step speed control and covered by an easily accessable filter, very nice). Front accessable 5 1/4" and 3 1/2" drives aren't removeable, but there is easy access from both sides to install the drive. Getting connectors into the top 5 1/4 drives can be a bit fiddly with a full case, but its not horrible.
Quality Stubs, not punch outs: Yup.
Easily pluggable USB port: Nope. You haven't seen it anywhere because the motherboard connection isn't standard. The only way to get a "one connector that works" is to have a passthrough cable that plugs in the USB ports in the back of the computer, but this is IMO worse than the "one pin at a time" problem. However, it would be nice if you only had to deal with the fiddly "one pin at a time" connection once, and then had annother connector in the line that is easily pluggable and unpluggable (they did this with all the motherboard connectors, so you don't have to reconnect the power/reset/LEDs/speaker each time you remove the motherboard tray). If they added the firewire and audio since I got my case, they may also have fixed this issue, but I can't find a review to be sure.
Bonuses:
Classy style. Its definatly not a plain beige box, but its not a overhyped flashy monstrosity. I simply hate the styling on the Xaser III cases, which is too bad since they're otherwise pretty decent.
The only sharp edge I've found is covered with a plastic guard.
The universal drive bay covers (sold seperately) are very nice. Completely cover the front of the drive with the same finish as the rest of the case, so my black case looks good with beige CD drives. Note that the non-universal drive covers aren't nearly as good, since it relies on very specific front covers and tolerances. Both of my drives just wouldn't work with the non-universal covers, and even if they had, they wouldn't look as nice as the universal covers. Also, there is no universal cover for a floppy drive, but its easy enough to chose your floppy based soley on how it'll match your case, since there isn't much else to differenciate floppy drives.
Easily snapped on and off cover, for access to the dust filter and fan speed control.
PS: Here's annother "holy grail" option (although probably lacking in front connectors): www.mountainmods.com Quite a bit more expensive than Lian Li, but plenty of space to work with and you gotta give it points for having 7 120mm fans and 4 80mm fans.