If you took too long to take over the points, the opponent will still continue to gain points even with only 2/5, possibly still giving them the win if they started taking them over early.
Your fault to not contesting enemy capping. On a standard map, you can easily cap 2 pts at 2 beginning and the opponent do the same. SO if he have such a huge point advantage that having 3 VPs capped still made you lose it only means that you barely win the main fight while your opponent was more focused on the victory conditions which are not only kill the enemy of the game. In other words you get outplayed and deserve to lose
If you've only got one or two line ships left, you can't hold three points.
You need 1 line ship at mid distance of 2 near points so you can react and contest when 1 escort come cap. with 2 line ships its 4 pts controlled
Most obvious point: Because it's a long, boring way to win
On your mind perhaps but sorry to burst your bubble : not everyone think like you and some people find very delightful to win against someone who only think about killing the enemy by focusing and the victory conditions.
As a side example : on LoL the victory condition is kill the nexus not have a high KDA ratio.