Regarding engine, they are the same but Toyota has done some changes. The new engine in Aqua/Axio is water cooled just like 3rd gen Prius and AC has no belt, these changes make engine more reliable. Moreover it is more easier to maintain; for instance in second gen Prius its really difficult to clean throttle body, its way deep down, it takes so much time to remove and then clean it same is the case with spark plugs, where as in Aqua the engine parts like throttle body, air filter, plugs etc are easier to clean or replace, as they are not hidden beneath anything.
And second Gen Prius was available till 2012 not 2014/15, so people can import them now as well, but they are really difficult to find.
I personally didn't drive Aqua, but my brother drove and tested it against our second gen Prius. He really liked Aqua but he preferred Prius over it because its more comfortable and gives a feel of a heavier more solid vehicle. But Aqua can be fresh imported where as second gen Prius must be impossible to find clean.