Imho:
I think the real problem is the armor system. Since it is generally a flat reduction, that means it is very difficult to have light-hitting creatures and heavy hitters when the player can have a variety of defense levels -- even if player defense from armor was fixed, you still can have +34 more from accessories and the defense potion. On normal that's a spread of 17 damage, which is a lot if you look at taking multiple hits. There wasn't any easy way to fix this, so the game evolved around avoiding most attacks. That doesn't work great for melee though, so they have more armor, but that still doesn't solve the overall balancing issue well, especially if you have ranged attacks from enemies over a large screen (when the melee guy has to get close)
This is always a tricky thing is systems where defense subtracts from damage taken -- they do not scale well. On small scales they are fine, which is why it works pretty well before hard mode.* But they just don't scale up indefinitely without really artificial systems. This is why you don't see that mechanic in a lot of games and tabletop RPGs. When you do see it, it is either kept small or as a means to say "you are going at the problem wrong" -- not as the main defense system. Percentile reduction of one form or another is easier to manage and balance, and can scale a lot better. They've added that in a bit for melee, but it doesn't entirely resolve the problem.
If they went from the ground up (so far Terraria 2 and hopefully Otherworld), I'd hope they use a percentile reduction system of some sort, with small, controlled amounts of subtractive reduction. Generally having incoming damage reduced by 50% and then improving that to 55% or 60% is a lot easier to deal with than having incoming damage reduced by 50 and that improving to 55 or 60. You can also do a lot to make sure that percentile reduction caps out at a particular value like 75% (giving diminishing returns, so armor still has value -- indeed, you can ensure that each point of armor has the same value in terms of Time to Live, which is nice).
I don't think resource management is a real issue here. Ranged classes essentially have resource BUSYWORK. Ammo isn't hard to get a lot of and keeping a huge supply is easy. It just takes time. Magic users are the ones that have resource management, and that's it. Basically, managing ammo only occasionally is an issue because of bad planning or forgetfulness -- something you hit your head about later but with proper prep waaay before battle is not an issue at all. Mana management is a constant thing during battle. Totally different -- not that I am a fan of resource busywork.
*Basically, subtractive systems have a range of values for which they work (depending on the system), and after that they require some brute forcing to ensure pretty strict linear scaling. This means making sure everyone fits into the right range of defense values. Do it wrong, and it either players can't stay alive or they die too easy.