Point matrix for ships?

It’s an art! so there isn’t one.

Back from holidays.

Well for costing skills you do have to estimate their impact on the metagame then their cost
a negative capacity would give you a -0.5 to -1pt
a minor capacity a 0.25 to 0.5pt
a major capacity a 1 to 2pts

For rounding unit cost up or down it will depend of usefullness of the unit and the other units already present.

For the basic cost, well it's bit more complex that's why the teams exist ^^

Here's a way of getting a basic cost but that's not the only way (and certainly not the fastest...)
Look for official units with the same stats or the nearest stats (AR, VA, H, Gun..., but not the capacities)
Remove the capacities costs from these units and add their new base costs together.
Then divide by units number, you will get an average base cost for the unit you create.
Add the capacities cost to your unit and then round the cost to the nearest full up or down.