Weapon charge times are hardcoded as stated above.. you can turn up the game speed which will increase the charge time, but it will also effect ship movement as well, ships will turn faster.. basically it just speeds up the game engine, not X effect of the game...
As for adding ships.. SFC 3 is capable of adding as many ships as you like.. you can rename races and so forth.. ask on of the mod makers such as nannerSlug or The Pelican on how to do this.. you can even change SFC 3 to have 4 playable races and 5 AI races for a total of 9 races.. also v531 has the ability to be modded so that you can add different weapon arcs.. damage of weapons can be changes as the effectiveness of weapons and armor and engines, etc.. just look through your CommonSettings folder at the *.gf files..
as far as adding weapons, adding more than 4 playable races, or changing weapon charge times.. those items are not changable in SFC 3, nor are they likely to become modable in any future patch.. a change like that would have to come from Activision, which since they are no longer selling the game, i would guess that they would say no to such a major change.. it would mean that the entire game engine would have to be re-written... and that is not about to happen.
hope that this helps...