Okay, to make this setup different from all the other homebrew mecha setups, how about we have this based on the Apparatus of the Crab? Which is to say, vehicles have their abilities be defined as using particular actions.
Additionally, multiple pilot positions could be present, each with access to different systems. So if you make a tank, you can have one person handle movement systems, another controlling the weapons and a third with control of energy allocation and communications. An actual proper crew with devision of duties by position in the vehicle. Defining seat position can be confusing, especially if it's by 3D grid, but basic coordinates with defined origin point works in most cases. Or you can just ignore AoE details and say they effect all the pilots.
Similarly, a combining mecha set can have each pilot be using actions on systems of their component mech. So a combining mecha with the left arm being a shielding and point defense covered pain in the ass to put down when separate can have those systems controlled by the pilot of that component mecha. If the right arm component mecha is covered in guns beyond sense, the pilot of that mecha controls those guns.
General structural actions, like permanent statblock movement modes and melee, can go to the largest mech or the one with a particular combining-mecha component active that has a restriction of one active. In the case of jump jet style temporary movement, controls on that go to whoever's piloting the component mech with the system, unless the combined mech has it as a permanent movement mode. Then it goes to the pilot with melee controls.
This idea allows for modeling a lot of things, particularly if you include tracking pilots and system as coordinates. Which could be streamlined by an internal floorplan to make it just marking where they are on a normal gameplay map, which lets you get out the Stronghold Building rules for making moving fortresses with plenty of helpful room functions. And tracking damage by wall segments you have to go through to start hitting important systems.
Internal floorplans means you can have troop transports have actual floorspace to put creatures on, making troop capacity be defined as "what can you fit in this floorspace?" rather than the existing standard of manually listing all the size categories. Said floorspace can have the exit be an actual, breakable, door with a defined break DC.
Having systems tied to use actions and pilot positions, in mecha without an internal floorplan, means being able to tell the guy with full BAB, ranged attack improving feats out the ass and nothing they can use while inside the mecha to go man the ranged weapons, while the caster with piles of construct support and the ability to inject more Energy into systems can sit in the pilot seat that controls rarely-action-using functions like defensive system Energy allocation so their actions can go to helping the mecha with their actual class features.
Furthermore, the mecha systems should ideally be defined as a type of partially customizable modules. For example, shield systems would all be one module with price rates for baseline Absorption and Recharge, as well as maximum energy invested in the system and a capped effectiveness per Energy. Having them be modules makes AI driven mecha be able to use cybernetic feats, saving lots of feat writing. Also, partially customizable Energy-using equipment for the Cybernetics classes that benefits from their Module buffing feats. And a means of spending GP for extra energy by stapling generators to everything.
In regards to AI driven mecha, I'd have the AI start off with just the normal standard/move/swift action setup at the baseline price. Energy investment for added actions, larger costs for automatic added actions and cost for mental scores. For PC use, I'd have LA based on non-HD GP cost. And have enough stuff attached to added HD that the RHD are worth class levels, like Str/pseudo-Con increases and more Energy. Maybe cap energy investment for extra actions to the highest mental score.
As for new feats, crafting feats are an easy one. Feats that give extra actions while piloting are another thing to use, as is gating mecha-module equipment energy investment behind a single feat to keep it from just being a flat upgrade over Modules at higher levels without needing to dig for extremely detailed balance or whacking the mecha system with nerf sticks. Pushing mecha-modules beyond their normal limits, like having either automatic Energy investment effect or boosted cap, can be another part of the feats.
With classes, I'd not like a dedicated mecha pilot class. Instead, I'd have the classes each be a different way of using the mecha system. The Artificer-equivalent acts as a living generator by relying on pumping lots of energy into the gear they make to make up for their lacking ability to use it directly. The class with power armor is crunched as using a mecha of the same size category as them, with bonuses to mecha-weapons, making them a good gunner.
The point of not having a dedicated pilot base class is that it leads to the meta-class problem. The Wizard is what's called a meta class, because it covers a large number of character concepts. There's rather few Arcane full casters in splats, specifically because the Wizard kills the niches by being too general. Sorcerers kill the spontaneous caster niche. Sure, you can have a Psionic pilot or an Arcane pilot, but a general Pilot class kills the idea of the dedicated gunner class, alongside all the other specialist roles you'd like for your low-fantasy/modern-day tank crew.
There's also the problem of mecha being larger scale combat, by expectation, so a dedicated pilot class can't do much in normal games. Having power armor be easily modeled gives the pilot something to use their abilities with, but then the class role is to be a durable frontliner, because power armor makes them tanky. They stop being a pilot class. So why not run with the compromises and use them for specialist pilot classes that have other roles when outside the mecha? AFCs can then remove the compromises and trade them for more dedicated pilot capacity, or even generalizing their pilot abilities. Or swapping the specialization altogether.