Maneuver Modes:
My main concern with this one is that is might 'pollute' the controls beyond the point of being accessible for some players. How often do you see new players struggling to even mange their power properly? Adding a second 'layer' to ship management might turn away potential players.
The idea of rams disabling terrain anti-collision measures is.. interesting. It might be a little 'too' punishing/unfun though.. for the same reason arming timers were added to nukes.
Faction Modules:
Unfortunately, I think the ship already sailed on this one.
Back before they added tiers to the game, I did a couple write-ups(with visual mock-ups) for proposals of potential 'progression systems' along the lines of what you're proposing. The core idea being that every ship would start with a specific playstyle in mind and you had to play those ships to unlock those modules and their variants. Likewise, certain manufacturers specialized in certain kinds of modules, but once you unlocked them, you could use them on any ship of the same class archetype.
For example, Rams and 'Pulse systems' were the domain of Oberon; Akula specialized in Nukes and 'modes'/specialty ammo. If you wanted to fit a Jupiter Destroyer(which normally specialized in missiles and jump/movement) with Goliaths and Weaponbooster Pulse, you'd have to 'learn how to use them' on the respective counterpart ships to unlock/earn those modules for 'global use'. (There was also the idea to unlock special factional coatings/patterns when you fully 'mastered' a ship and all its available modules as an extra incentive to keep going.)
I thought that was a much more attractive progression, tutorial, lore-immersion and monetization system to keep players/customers engaged than the Tier system we wound up with.. but the people in charge decided otherwise.
(Monetization Note: Hero ships would come with special fixed loadouts that were a-typical of their manufacturer - like a Scramble Pulse Akula Destroyer with Evasive Maneuver - in addition to the cosmetic perks. It would allow players/customers to buy into interesting playstyles before investing/inspiring the grind required make a custom loadout for that chassis.)