Agreed that a unit with a weakness should be taking more damage than one that's neutral or has a resistance against your unit. However, the units are designed around base stats, where terrain and unit bonuses actually make a difference. In these instances, the bonuses would add up to cause the Scimitar to take more damage from artillery than a Sub. It's only once you factor in the huge military bonuses that are becoming increasingly common that the math starts to break apart.
At 0% bonus
Scimitar: 200 defense
Sub: 140 defense, 70 Dug In bonus, 150 defense against artillery = 390 defense
Turturret: 170 attack, 120 bonus against light = 290 attack vs light units
At 200% (x3) bonus
Scimitar: 200*3 defense = 600 defense
Sub: 140*3 defense, 70 Dug In, 150 artillery bonus = 640 defense
Turturret: 170*3 attack, 120 light bonus = 630 attack
As you can see, once you start counting bonuses, the base stats start to heavily eclipse whatever bonuses the unit may have. The 190 difference in defense between a Scimitar and Sub (against artillery) shrinks to only 40 at 200% bonus, and the Sub actually has 30 LESS if Dug In is factored out, compared to still being 120 ahead at 0% bonus. Likewise, the Turturret only has 30 more attack than a Scimitar's defense compared to 90, and 130 less attack than a Sub's defense compared to 220. I know this is a lot of numbers, but the fact is that if you're playing with and/or facing units with strong boosts, the bonuses become practically irrelevant. Everything becomes equally effective against everything, as strengths and weaknesses become heavily blurred. The only abilities that really matter now are flying and stealth, as no amount of stat is going to help against those abilities and they must instead be countered by other abilities/units.
A solution to this growing problem would be to have unit bonuses and abilities scale with military bonuses as well, which should help to preserve the strengths and weaknesses that each unit is intended to have. That, or simply change the numerical values to percentages as is done in Elvenar. For example, instead of Subs having a 150 defense bonus against artillery, have them take 50% less damage from artillery instead (this number is only an example). But in both of these examples, it shows that percentages are much better at scaling to the situation than flat, unchanging numbers are.
Finally, going to tag
@Zarok Dai for this part. Since it hasn't been brought up/talked about for a while I'd like to once again push the suggestion that a unit's speed stat be made visible in-game. Is this something that's being worked on yet? Considering almost every unit in OF has a speed stat that does not match its movement, it's becoming very confusing to actually keep track of turn orders if you're someone who's used to the 'movement = speed' design of previous ages. I realize that making this value visible requires some tweaking of the in-game tooltips, but I feel like it's high time that it happens. Is the UI adjustment the only reason why it hasn't happened yet?