Drone speeds and plasma speeds were the product of playtesting on a hex map. Because of the geometric nature of a hex grid, and the control a player has by choosing which hex a drone should move into given a choice, the actual distance covered in SFC is further than SFB because the seeking weapon tracks its target in an arc. To compensate for this, seeking weapons were given a speed increase.
Double internals were added to the game simply to make it last longer. Imagine if your ship, in SFC, could only withstand half the damage it does now, most battles would be over very quickly.
The spare parts are an extrapolation of Emergency Damage Repair in SFB, which was a number equivalent to the Damage Control rating of a ship. Typically it would be 4 for a Heavy Cruiser, and this was the number of systems a ship could repair in battle. Allocating one point of power to a 'repair' system would also make repairs but these were unlimited. Repair systems are usually only found on Fleet Repair Docks and some PF Tenders, although did appear rarely elsewhere as well.
I would imagine the number of spares was increased again to the give the game longevity in combat. Unlike EDR however, spares can only be used on systems you can click on. EDR could be used on anything eg. Hull, Labs etc. The Damage Control rating of a ship also determined how fast shields would repair, not Labs as it is in SFC.