Shields vs. armor is a choice that often depends on the ship (if the ship has many mid slots, then it’s intended for shields, if it has many low slots, it’s intended for armor). Typically, Caldari ships are intended for shields, and there are also a few Minmatar ships that have many mid slots, and a couple Gallente ships that have 4/4/4 or 3/3/3 slot layouts that allow the versatility to use either shields or armor.
In general, shields are somewhat instant gratification (the shield booster repairs your shields as soon as you push the button, unlike armor repairers where you have to wait the couple seconds until the END of the repairer’s cycle). Shields increase your ship’s (radar) size slightly, making you take slightly more damage from missiles. And active shield tanks require a robust capacitor recharge rate.
As far as missiles vs. rails, missiles are preferred for PVE because you can load the missile type that will do most damage to the NPC, AND because the NPC’s don’t run away while your missile takes forever to get to its target. Guns are preferred for PVP because they hit instantly; enemy doesn’t have time to warp away, at least on the first shot (which is often all it takes).
So, to answer your question, if you’re planning on doing PVE, then missiles are the way to go. Make sure you train enough electronics to be able to use a Target Painter module for missiles. The Caldari missile ships are very popular for PVE / missions.
The Gallente drone ships are equally popular, if you’re wondering, for the following reasons:
- drones can be loaded to do the damage that best hits the NPC targets (like missiles)
- the ships are versatile to allow many kinds of fittings, including one where the guns are removed in favor of LARGE armor plates or shield extenders
The mission agents used to have preferences, long ago, to give you missions related to their Empire (Caldari agents would give Guristas missions for example), but a few years ago CCP revamped the missions to be randomized. So now you see any of the pirates, plus (neutral) mercenaries, criminals, drones, etc., where it doesn’t really matter which agent you do missions for (as far as mission selection).
In wormhole space, the PVP hunters will immediately peg you as a shields-and-missiles ship if you fly the Caldari Kestrel or Caracal. On the other hand, if you fly the Gallente Tristan or Vexor, they’ll figure out “drones” but won’t be so sure what defenses and PVP capabilities you may have, so you get a slight advantage.