Skills are the stats, based on a tier system instead of raw numbers.
Vigor acts as an energy pool much the same as a mana bar in most RPGs. It doesn't determine how strong your abilities are, it's how many times you can use your abilities.
Latens is what you spend to purchase tiers in different skills. If you have 250 Latens, you can obtain a Novice-tier skill (Soldier, Engineer, Duelist, Tamer, etc). Each tier needs more Latens to obtain, and once you have to 'spend' your Latens for every tier. If you purchase that Novice-tier ability, your Latens goes back down to zero, and you have to build up again.
Vigor is basically the sum of all Latens you've obtained with your character. Latens is how much bank you have to spend on skills. The tier you're at for a skill determines how capable you are with that particular skill.
In regards to natural capabilities (i.e. speed, physical strength, etc), it's an even playing field until other abilities modify them. A Demvir is as resilient as a Laicar at base, but their Machina Body ability increases their resilience beyond base level (just an existing example, there are a number of others).