Blah, wasn't going to post anymore, but I can't resist....
Anyhow, just because there is the indication of a leveling mechanic doesn't mean it must relate directly to command input sensitivity and aptitude for success.
One example would be you get your starting list of mechs depending on your house. As you level up, you get more mech options from each weight class of mech, or choose them individually to find the frame and base load out you prefer to suit your play style. A system like this assumes a very limited mech lab or the lack of a mech lab in order to curtail certain weapon combinations that could be deemed problematic depending upon how detailed of a shooting mechanic system they implement. They could open up options for battle armor, support vehicles, or aerospace fighters using this style of implementation as well. The representation in game would be certification for use, or rise in rank and being trusted with more equipment options (as much as I'd like to see the ability to fine tune a machine for personal use, I fully acknowledge this might not be a balanced or feasible option for the dev team).
Another example could be weapon grouping and independent targeting options. For example, you start off with 1 weapon group and get to choose to chain fire or group fire (alpha strike). As you progress, you get more group designations to break them up in order to use like weapons or similar function weapons more efficiently. Then allow hud point designations for each grouping as suggested
here. This would allow a savy player with appropriate character skill to split fire simultaneously or setup lead points for flight time vs hit scan weapons along an anticipated opponent movement arc.
Another example could allow for more "advanced" physical maneuvers with the machine. This could include unlocking anything from simple short hops to clear small obstacles, crouching, covering the body with arms, etc.
Another example could be dictated by support equipment options, such as potential masc duration/mech shake or stability while in use, the number of weapons controlled by a C3 master/slave system, or implementing ECM/ECCM in cockpit mini games to represent levels of radar jamming or other interference and convey mild bonuses to the total length of operation within the game.
If they were to go the route of potential passive bonuses, they could implement heat tolerance and blackout/redout levels for the pilot making it harder for the pilot to shut down temporarily (similar to mech shutdown) in high heat situations (could be a mini game here too to "wake up") and adjust slightly the start up and shutdown times of the mech.
Basically anything that would be directly out of the player's control or somewhat indirectly out of their control could be adjusted or opened up for use through a cert or passive bonus system and going this route should be simple enough to allow for enough options to give folks a feel for specialization. Although re-certification should be an option in order to keep the game down to 1 account, 1 character. There is no need to encourage multi-boxing or multiple accounts for a single person.