The ninja perk doesn't really give them a huge boost either unless you dump all your points into it. In this game I wonder if going up the luck tree and using critical attacks would ultimately be more effective in pure damage output. If I could reroll with a new build I'd only take intelligence high enough to get "gun nut" and go higher in luck and take the "idiot savant" perk for experience and perhaps go for critical hits. I'm not a big fan of "banking" criticals... or telling the game when I want to use them. Critical hits should be random, based on dumb luck and where the shot lands.... I've found the VATs system to be rather hit or miss as well... shots in vats that supposedly have an 80% chance to hit and missing 3 out of 5 of them happens more often than it should... or having a 60% chance to hit and missing all 5.... maybe my perception at 5 is the problem?
Science is needed for some gun mods and for energy weapons though... I haven't played enough of the game to decide if the tradeoff in intelligence would be worth it yet... if I'd be happy without the "science" perk.