Id rather keep the use of aptitude incompatibility low, and dont quite want to encourage adding to many of them through other mods either. The more free the system is, the more fun it is too.
So for now i will likely just keep it at Automated & Logistics, as those are aptitudes where i can generaly see it be needed.
Its not that much of an issue if aptitudes have some overlap, you just should not design aptitudes that have 1 to 1 overlap with an existing one, and that becomes a lot easier by making the aptitudes focused on multiple topics at once, for example for the Exotech tree i wanna do at some point it will handle things like phase, carriers and a few generic tech related things. So there will be some synergy with the Strikecraft Aptitude, but since its only a few carrier skills you wont get to overlap to many carrier skills.
I understand the idea of keeping the system open for players, but I'd like to point out that the inability to prevent certain skill synergies makes designing and balancing aptitudes harder, which in turn could lead to less choice for players.
Just as an example, imagine if aptitude skill tiers and per-tier limits wasn't a thing, and players could take any number of skills together the moment they have the points. Would that make creating and balancing new aptitudes easier or harder? And if it did make creating new mod content harder, would that ultimately give players more or fewer choices? I think it's a lot easier to make new content that's conceptually novel and balanced compared to just one aptitude, rather than all nine at the same time. The system is fantastic and I want to make new content for it. Ultimately I'll work with the design constraints I have, but I believe more choice for the modder in which balance levers to use gives more opportunity to make good content, so I hope you'll give my suggestion some more thought.
Anyway, whether or not you make the change, I'm still enjoying the system a lot. Good job.
I get your points, but i do just think the quality is better with incompatibility avoided where possible. I think the way the system works is one of the more meh parts of the mod, but just required for certain things. In the end, even overlapping aptitudes with similar skills means that you are giving up 2 out of your 3 slots, so you are still going to miss out on stuff. Thats why i think its just best to avoid making aptitudes that are hyperfocused (Like Strikecraft, Smallcraft, Automation) if they are already around in the main mod, and instead focus on more varied trees. Like if a mod wants to add a unique XO for their faction, it can try to have skills based on the multiple features that define the faction.
That said, if theres any aptitude you think you do really want to be able to make yours incompatible with, feel free to say that here. Though i dont think i would add a category to any of the more generic stuff i.e Management, Technical, Tactical, etc.