Based on number of boundaries...!! Really..?!! Where did that come from? 
The rules of the competition - sure you might consider other options, but I don't see why this is necessarily problematic. Both sides knew this from the outset, and both sides therefore knew that were the super over to end up level then England would win as they'd scored more boundaries. When NZ batted in the super over they knew they needed 16 not 15 to win, hence the desperate (and unsuccessful) attempt at a second run off the final ball.
If you should have a winner...
Of course you need a winner - it would be bonkers to go through a 6 week tournament and end up in a situation where no-one won.
..the NNR/the position on the points table would have been more appropriate.
That would be a possibility, but I disagree that it would be better. The approach adopted meant that the winner was decided entirely on what happened in the match yesterday between the 2 finalists. Being higher on the points table has an advantage in that your semi-final opponent will be a lower ranked team on the table (not that that proved to have any effect) - beyond that all teams should be equal and the winner should be decided purely on the performance on the day.
Can you imagine had it been decided on table position (therefore England would have still won) and New Zealand would have quite reasonably pointed out that had it rained on a different day then NZ rather than England would quite likely have won. I'd prefer to decide the tournament winner on the basis of cricket rather than rain.