If both characters are gaining abilities that support their archetype, and the non "mage" (non-magic/non-engineer/non-psionic/non-initiator) character is gaining two abilities where the mage is getting one, and both abilities are probably stronger than the one ability the mage gets.
Spells are pretty much the ultimate class feature so this should be easy to balance.
Restricting things to two per level has the added feature of keeping things simpler, though these features having more than one application (or modifying/improving multiple abilities).
This is harder to account for; Chassis is not really an "ability" so much as it is "what the abilities are tied to", or "how they pay for an ability". You can't tie it to an extra ability because it's not tied to a class - You don't get BAB +6 as a capstone, you get it for having 1 level in any class which a full BAB.Effectively, the mages would get one unmarked ability, while the melees only get an equivilant when they hit +6 BAB.
It's more subtle with Hitpoints, skill points and saves, but it's there.
My only issue would be the difficulty getting multiple small things to compare "evenly" to few "big" abilities, but I'm willing to give it a go."Any given level should not be more powerful than any other level." So a collection of weak abilities would be on part with a new spell level and a minor boost. Seem good?
This is an archetype capstone, not a base class capstone, and I would be strongly suggesting any level 4 spell is chosen from a very narrow list.Also, the capstones for casters are not the level 3 spells, they are the level 4 SLAs.