Can the reaction intermediate be lower in energy than the reactants or products?
The intermediate is a proper chemical species but a reactive one under 'normal' conditions and is not a transition state, i.e. it has a short, but measurable, lifetime. The intermediate can change only by crossing one of two transition states, one back to reactants and the other to another intermediate or to product.  

Any intermediate must not be lowest energy species, including reactant and product, but can be lower or higher in energy than the reactant (but less than any transition state) and higher than product. The limiting activation energy will be the largest one in the whole scheme, so may be that between reactant &amp; intermediate or between intermediate &amp; product. Which it is depends on the exact species involved.