We are in the late design stage for our new house. The house is quite large and will need to have a septic tank.

I personally don't know much about septic systems, never had one before, so I'm copy and pasting some info I just received from the engineer:

"This will be a low-pressure dosed system because the drainfield is over 1000 sq ft.  Also, there is a clay layer at about 46 inches below the ground surface.This means that the drainfields will be slightly mounded because there needs to be a minimum of 54 inches separation from this layer.The mound height will be on the order of 20 inches above the existing grade."

This just doesn't sound very pretty to me, so we are looking for alternatives to avoid this huge drainfield which would basically be in our front yard.
Are there any?
What about a graywater re-use system? Would this significantly reduce the size of this septic drainage field ... or anything else we could do?
We are a little bit on a budget here, but if we can make this look better and of course at the same time be more green I certainly don't mind spending some extra money.

I don't know about other state rules other then connecticut.  Basicaly there are a series of things that affect the size of the system and its requirements here.

1.  # of :"bedrooms" in the house. Any room that is not a kitchen or a bathroom and bigger then about 6X8 that does not open directly into another bedroom only is a bedroom acording to the rules.  This sets the design load of the system basicaly in gallons per day.  

2.  Level of high groundwater in the area  ie the mottling depth.  This is determined by  deep pit tests in the area of the system.

3.  The soil strata  ie clay is not very penetrable so any leaching must ocurr above the clay layer.  This is also determined by the deep pit tests

4.  The rate at which water percolates through the existing soil "PERC TESTs"

Based on these things the engineer designs a system that meets the design load.  These are fairly simple calculations.  There are also a number of different Engineered products that can reduce the size of the system (but not necessarily the depth).

when a system excedes a certain daily design flow rate, they are usualy done as a pumped system that releases efluent 2-4 times per day.  for some reason that works better then continuous drainage.

Here  You can have a seperate graywater leach field, but it is in addition to a full sized septic system(I think)

I don't think you are going to reduce the height of the system much if at all.   First they have to scrape all the topsoil off  in the leach field area.  Figure at least 1 ft of material deep.  then they will replace it with septic fill and build it up so the bottom of the pipes are  54" above the clay  so 46"-12 =34" so you will need to add 20 inches of aproved septic fill then the leaching pipes then more sand to cover the pipes and then the topsoil is replaced.

You are probably looking at 1000+ yards of septic sand so it is not going to be cheap. 

So What can you do? 
First consider a house redesign.  Can you change the number of rooms used to calculate the size of the septic system without changing the way the house works for you?  Simple things lilke 4 ft wide openings with no doors to the study might help or have some rooms like master closets only open into other bedrooms etc.  Bonus rooms over the garage are also counted if they open into the main house but not if they open into the garage only. 

You could also go to composting toilets and possibly reduce the leach field size dramaticaly.

In other states I have no idea what the rules are.
Cheers,
Eric