I wouldn't be surprised to see some clever nods to classic ship abilities. I feel they'd be limiting themselves if they couldn't borrow and adapt some of the elements from the original and reinterpret them in a modern context. I would be surprised if there weren't ships with automated attack drones and other homing weapons. Add to that warping abilities, different types of propulsion, stealing energy/crew, disabling an enemy's systems, etc. It would probably be harder to come up with new ship designs that don't inevitably borrow some of those attributes than it would be not to.
It's my hunch that ship design in general will be more open-ended and not limited to a specific set of preconfigured designs as we're accustomed to. I picture ship configurations being more modular and any discussion of what ships can and can't do may become more of a gray area because weapons and abilities will be more interchangeable than they were in the original games.
P.S. Mashing the the buttons after losing a Pkunk Fury had no impact on reincarnation, it was just a 50/50 RNG coin toss.