In a PHP web application I'm working on, I see functions defined in two possible ways.
function myfunc($arg1, $arg2, $arg3)
// where $array_params has the structure array('arg1'=>$val1, 'arg2'=>$val2, 'arg3'=>$val3)
If the system is changing so often that using an indexed array is the best solution, I'd say this is the least of your worries. :-)
In general functions/methods shouldn't take too many arguments (5 plus or minus 2 being the maximum) and I'd say that you should stick to using named (and ideally type hinted) arguments. (An indexed array of arguments only really makes sense if there's a large quantity of optional data - a good example being configuration information.)
As @Pekka says, passing an array of arguments is also liable to be a pain to document and therefore for other people/yourself in 'n' months to maintain.
Incidentally, the oft mentioned book Code Complete examines such issues in quite a bit of detail - it's a great tome which I'd highly recommend.