Both are 2000cc conventional diesel engines. They say the later models got some improvement; i.e. less noise and smoke and more durability while fuel economy remains almost same. Generally speaking, corolla diesel has good engine life (if properly maintained) and you don't need to wait in long ques for petrol during CNG off days, plus the millage is also better than 1.6 manual.
Wait for the experts who will explain everything in detail 
Btw are you going for engine swap or buying a new (used) 2.0D?