The way I look at it, it is not the kilograms alone, but the percentage of overweight that is required to be looked at, as far as weight reduction is concerned. There could be many reasons for the overweight.
When you do the design of the aircraft, at the initial stage itself you have to calculate the approx weight of the fuselage, wings, empennage, engine, oleolegs, hydraulics, fuel, seats, interiors and a host of other things. Fine tuning is done while designing individual components, and again calculate/readjust the weight of individual components viz., fuselage, wings....Aerodynamics group and structural engineers normally have a clash of interest. Aero group try to reduce the drag as much as possible and the structural group, the weight of the craft. A classic example is the wing itself - a thicker wing is lighter, but the drag will be more. Hence you should select the right airfoil section at a very early stage in design, since it has a lot of influence on the rest of the design/performance of the a/c.
Descrepancy arises in the calculations due to various factors. One of the reasons is that commercially available sizes may not match your DESIGN values..For eg., if you have arrived at a figure of say 0.8 mm thickness for the skin of the wing, it may happen that commercially available sizes are either 0.75 or 0.85. In that case you have to go for 0.85 mm (not 0.75), which increases the weight (ofcourse for mass production for Boeing etc, one can demand dimensions closer to their requirements). Same goes with structural components. Also, it may not be possible to fabricate components exactly as per the production drawings. All these invariably add to the weight.
Yet another reason for increased weight is that, in prototypes, factor of safety may be a little higher. In aircraft industry, about 1.5 is the normal factor of safety given and there is not much room for complacency.
In the case of Saras, it was well known for the designers long before that the craft had a overweight problem. They were trying to rope in the Russians. Where exactly is the problem, I don't know. I also don't know if it is a question of setting high standardards and not able to achieve it. In any case, the excess weight is almost equal to the payload of the a/c. Unless the weight is drastically reduced, commercial viability of the a/c will be doubtful.