So to summarize what you're trying to do, you have a class template:
template<typename RL> class RegularLanguage {...};
with some methods implemented and others only declared, but not implemented.  Then you try to derive from this and in the derived class implement those other methods that weren't implemented in RegularLanguage:
class FiniteAutomaton : public RegularLanguage<FiniteAutomaton>
You seem to be conflating two concepts in C++:  inheritance (specifically, polymorphism) and templates.
Your assumption was that by inheriting from RegularLanguage you can implement the missing stuff in the derived class.  That's not how templates work, but polymorphism does work that way.  You need to either:
- Fully implement all methods in the class template RegularLanguage, and then deriveFiniteAutomatonfrom that.
- Make RegularLanguagean abstract base class -- not a class template -- with (possibly pure)virtualmethods, and derive from that.  The methods you want to be implemented inFiniteAutomatoncan be.  Those may or may not be pure.  The methods you don't want to implement in the base class should be declared as pure (=0), and then implemented in the derived class.
It sounds to me like what you're really trying to do would be better accomplished with #2, so here's an incomplete example of how to do that:
class RegularLanguage {
public:
    virtual RegularLanguage* Clone() = 0;  // Creates a copy of this object
    virtual RegularLanguage& complement() = 0; // pure virtual must be implemented in derived class
    virtual bool containedIn(RegularLanguage& super) // non-pure, does not have to be implemented in derived
    {
        return intersectionWith(super.complement()).empty();
    }
  virtual ~RegularLanguage() {}
};
class FiniteAutomaton 
:
  public RegularLanguage
{
public:
  RegularLanguage* Clone()
  {
    RegularLanguage* clone = new FiniteAutomaton (*this);
    return clone;
  }
  RegularLanguage* complement()
  {
    RegularLanguage* comp = this->Clone();
    comp->SetSomeStuff();
    return comp;
  }
};
There are a number of details hidden up there that I haven't mentioned.  For one, the return type of complement is now a RegularLanguage pointer, rather than a RegularLanguage by-value.  This is required1 in order to avoid the so-called Slicing Problem which would break polymorphism.
For another, I have abandoned the use of templates here because as I've implemented this, there is no apparent need for them.  However the use of templates and polymorphism are not completely mutually exclusive.  The base class could employ templates, and in fact the base class could be a class template and still be an abstract base class.  But the derived class must derive from a concrete instantiation of that base class template.  Things get somewhat complicated here.  Just be careful that you're not seeing everything as a nail and get carried away with that hammer.
For another, I didn't implement a virtual destructor in the base class before (this is fixed now) but you must2.  Just remember this:  if a class is intended to be derived from, it should have a virtual destructor in virtually every case.
For another, I've added a Clone method to the base class as a pure virtual.  This was in response to the suggestion that complement() shouldn't return this instance of the object, but a new instance which is the complement of this instance.  In a polymorphic hierarchy, when we make copies of object we almost always need to do so through the base class pointer, so a Clone() type method is usually present in such a design.
1 "This is required [passing by pointer]:  Actually, you could return a reference as well.  Return a reference if you can, but here we need to return a pointer.  (Actually we should be returning smart pointers, but that's a tangent.)
2 "You must [implement a virtual destructor]:  Technically, you need to have a virtual destructor if you intend to delete the object through a base class pointer.  I have never in my professional career seen an instance where I could not or should not implement a virtual destructor in the base class of a polymorphic hierarchy.  It's close to correct to say you should always do this, even if you have no plans to delete through a base class pointer.