The pilots were under huge amounts of armor, and we're more then protected; probably the most protected thing on board. The Kaiju never had an easy time killing the pilots, and only really won when they double teamed them AFTER being specifically "updated" to defeat them (or surprised them with updated stats like in the opening fight).
Also, on the ranged weapons, this is obvious but I'll spell it out like del Toro did in interviews many months ago. Kaiju aren't just stupid animals. They think, react, and move accordingly. How do you plan on shooting missiles (large enough to do more then tickle) at something that can think and dodge accordingly? You don't, that's what. You build giant fucking robots and smash them the fuck up. The only jeager that had missiles only ever used it as a finishing move because kaiju would just duck, weave, and hide from them. This is also evident when Gipsy fights in the city and the Kaiju says fuck this and hides among the buildings for some breathing room.
And on the electric/nuclear thing, personally I wouldn't want to rely on dangerous nuclear power especially if I risk total destruction when fighting a kaiju. Doubly so if I often fight in populated areas. Just seems... Silly if electric always got the job done prior to the actual fights in the film. You gotta remember, we come into this universe almost a decade after the fighting began, electric jeagers have a better track record then nuclear.