I've noticed weapons have a gauge on them like "0/99999" which fills up with more use. No clue what happens when you fill it up, though.
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Yeah I prefer the bolt-action, but there are some situations where a semi-auto sniper turns the game into easy mode which is why I always carry one.
In terms of modding/bonuses for the rifles.
Bolt: Crit Barrel (not damage barrel because the crit multiplier is higher). Scope is your preference. Mag increase not reload as by the time you need to reload with an extended mag, you should already have another weapon out anyways.
Semi: Damage barrel since you'll find yourself able to go for more non-crit shots at times. Scope is your preference. Reload speed instead of mag size because you already have a decent clip and at around 10-15 sniper shots, you should probably already be pulling out your LMG.
thats a weapon xp bar.. there is an other xp bar on your character that levels when you use any of that weapon type.. as the weapon and you level up in that category, both do more dmg.. BUT.. if the weapon is capped on xp, YOU will no longer gain xp in that weapon type.. so once you max out a weapon xp, swap weapons and keep leveling until YOU are maxed.. then go back to your best one..
or..as you level don't try getting the best thing yet.. simply level up the crap along the way to assure you max out that weapon type, and then go hunting for your BiS pieces.
For a good Bolt Action - Damage and Crit Multiplier, Fire, Shock and Radiation are good. Recoil is neglible, Bloom is irrelevant, mag size doesnt matter.
For a good Semi-Auto - Damge, Crit, and Recoil. Mag size is a good consideration, Radiation is probably the best.
but in most cases, just put the best mods on the rifle as you can. The mods are pretty specialized so it is kinda hard to go wrong.
No, it's because progression is horizontal. Basically most bolt action sniper rifles have a damage of 1257 or 1000. You won't find like a 1245 or a 1034 or something like that, so the weapons you get from the very first quest are just as strong as weapons you get from a tier 4 lockbox at level 2000. It's just a matter of very tiny upgrades from mods that make them better later.