there are 4 main skills I suggest you level up thought not necessary: Health = increase your Health Points and health regeneration speed while passive Fitness = increases your running speed and crouching speed. Firearms = increases accuracy, reload speed & disarm chance%
Violence = increases dynamite, molotov & TNT load as well increase crew HP. ( not that important helps with safe strats against crowd control or speedrun killing ambushes)

the rest of the skills aren't useful for speedrunning except Negotiations for Don% & Don of NYC%