> My main peeve with matlab is that to write a function it
  > is required to make a separate file however most problems
  > that are solved with matlab don't really need functions 
  > in the first place. 

That's just where the madness begins! My current pet peeve is that you can't index the result of a function directly:

  x = 10:-1:1;
  
  a = sort(x)(1:5);   % illegal!  
  
  tmp = sort(x);      % depressing :(
  a = tmp(1:5);       

  f = @(x,i)x(i);     % a little better
  a = f(sort(x),1:5); 

Every release gets a bit better, but there are still a lot of strange historical limitations.