Although Qshake has already expressed his contrary opinion elsewhere, I without doubt will rely in FEM packages to model foundation items that are not inmediately amenable to well established designs. The reason for that is that with some software packages yo can model the thing in minutes, and get good appraisal on what happens; also the flexibility of the mat or pilecap is immediately discounted, since the bending plates inmediately accounts for it.
When ground is involved I have modeled the thing as both Winkler springs and as plates of soil laid vertical under our foundation, or around our piles or so, all over a unyielding rock layer at depths bigger or at least in the magnitude of the building height.
All the stiffness bussiness in this case is passed and gauged through modulus of young etc. By the way that to model the things in ways that the settlements be credible one has to use stiffer modulus than those usually promoted for soils...the same thing that happens with well compacted highway top layers: are more stiffer than usually assumed.
Of course all this is incorrect, but through bracketing of the stiffnesses and changing your input member or plates you can get readily an envelope of design items compatible with what expected for settlements etc, that you can evaluate separately.
This same thing but well done is what one should expect of soil-structure interaction programs. I have not one such available, so I proceed this way for irregular shapes, investigation, and design with bracketing or safe assumptions such the dismissal of soil stiffness. For springs horizontally I use to take 1/2 or 1/3 of the vertical stiffness.
This is not to say that I don't use ready-made solutions to element-type designs; I have bought and made lots of programs for such thing and I do. But I am not hesitant to proceed this way, and I am not alone; for example for soils with heave or significant settlement it is accepted, yesterday I read the "complete" dismissal of any "ground" contribution to support the vertical loads, the total bearing on piles (which by the way is the usual way in which we design pile-caps).
ALso note that if in a high risk seismic zone battered piles are not recommendable.