Doesn't matter to you!
Have secondary weapons retain the ammo you picked up for it while it was active after a weapon switch in Story and Explore modes. The ammo loss when switching secondary weapons was the only thing that slightly bothered me about Destiny everything else I think is damn near perfect as is. This kind of breaks story and explore mode for me. If I choose to carry an Auto Rifle, a Sniper and a shotgun because I am traversing a wasteland where I may need to make a long range shot, and then have the shotgun when I am rushed by hive in a dark room and an auto or scout rifle for more manageable situations then that is the choice I made. If people are worried about PvP then just only let the weapon you have selected in the Primary, Secondary and Heavy weapon categories enter into PvP. Otherwise I do not need 10 slots for weapons, just make every weapon I pick up through the game go straight to my vault and make me trade it out when I am in the Tower. 1 primary, 1 secondary and 1 Heavy. Having the ammo you pick up for each gun stay helps, I have no issue with the fact that it only drops special ammo for the secondary weapon I have active, that is fine, I like that, but the ammo I already pick up, in story or explore mode especially, should stay in the gun when I switch weapons until I empty it by shooting it. If I am out on a hunting trip and I switch from my scoped rifle to my shotgun the ammo doesn't magically disappear, and I will not carry 50 or 300 rounds of ammo for a weapon I did not bring with me either. For me having the ammo disappear kind of violates a sense of "reality" they have brought to the game.
Edited by xAT 117x: 8/1/2014 9:23:28 AMIt is designed this way so that you can't be surprised by a situation, and instantly switch to the perfect heavy weapon for that situation. There is a simple way to overcome this. You mentioned in your OP that you plan ahead and take a Sniper and shotgun into the wasteland. All you need is a bit more planning, and take several Special Ammo synthesising packs with you. This way when you want to make a switch you can get the ammo you need. EDIT: Also, with the amount of weapons you can carry there really is no "choice". You can carry a Sniper, Shotgun and Fusion Rifle; plus a LMG and Rocket Launcher; plus one of every type of primary weapon. You are not making a choice about what you 'might' need. If the ammo carried over, the game would be ridiculously simple.