Thrusters, counter-measures and missiles are still being moved over to Item System 2.0. Power plants were started for 3.2 the next steps to be implemented include item degradation and the resulting loss of performance associated with that.
Quantum acceleration and speed is currently determined by ship size, the ship drive size and the mass of the ship. This was done on purpose to emulate a more cinematic ‘warp-in’ scene. At the moment the bigger your drive, the faster you accelerate and the higher your top speed but the drawback is longer cooldown time and longer spool up time.
Implementing a more PU-esque battle mode in Arena Commander might be implemented fairly quickly in theory, however some of the issues against it would be a fluctuating number of players, which would slow down flow for the players as they may not be able to find a full match straight away. Balancing would also be very hard to do. CIG are still looking at a dedicated team for Arena Commander and Star Marine but are not ready to announce anything for that yet. The focus is the PU and the player numbers reflect that. It is an idea that CIG like so it is not entirely off the cards but it is not something players will see any time soon.
With the upcoming release of the Hammerhead in 3.3 CIG will be adding more difficult missions. These missions will be intended for larger ships wielding more firepower that smaller ships or small groups of players should (in theory) not be able to complete as opposed to using the same missions but scaling them up for a larger ship. Adding in more and harder missions will also allow groups of players that want to try the harder missions in smaller ships the opportunity to do so. This harkens back to the greater the risk the greater the reward philosophy. Interdictions are going to be balanced though, as these are not something a player chooses to do. For example if you are in Aurora and pulled out of warp via an interdiction then you won’t be facing a Hammerhead.