Paying 3 points to increase stats means you often end up with one or two leftover points that you can't use. This is reminiscent of one of the bad things in Dominions, where you design a leader and end up with leftover points you can't use.

It is extremely annoying. If everything costs 3 points but a few special abilities which cost 5 and 10, then divide all costs by 3, round 5 to 6 (/3 = 2) and 10 to 9 (/3 = 3) and give only one third of points. Counting in 3's is uninteresting.