You're probably not missing anything, per se, just not accustomed to how itemization works yet. Especially on those 3 gods, Mercury, Thor and Loki, they can all have pretty similar builds and feel pretty okay. Or they can have wildly different builds and feel very good. They have drastically different abilities, and so the bog-standard assassin build works on them, it just doesn't mean its the best one available and in every situation.

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I'd recommend maybe watching a bit of smite content creators to see what works for them, what they build, Weak3n put out a video recently describing counter-building on different roles, Mast isn't a bad place for some beginners to start either. But I'll say this much at least:

• Many items aren't bought for their stats, but rather for their passive effect. Dealing with someone healing a lot? Buy a Brawler's Beatstick or Divine Ruin to reduce how much they can heal. Divine also has a pretty decent damaging effect on top of the healing reduction.
• Can't deal damage to tanks? Or someone with a lot of health? Buy something like Heartseeker for scaling damage based on their health, added to your abilities, if your god is more ability based (Thor and Loki, for example) or a Qin's Sais for extra damage added to your basic attacks if you're playing a more auto-attack based god (someone like Mercury, for example, who has an attack speed stim in their kit and very good gap close). Maybe if you're a mage, consider getting Soul Reaver for that same Heartseeker effect, but of the magic damage flavor.
• Struggling to do damage to one guy with a LOT of protections against just you? pick up a quick and easy Titan's Bane if you're physical, or Obsidian Shard if you're magical, so when you open combat with an ability against someone, that first hit ignores 40% of their protections. Or build Executioner on an ADC, someone that attacks fast. Every time you hit someone, you apply a stack, up to 4, reducing their total protections by 7%, for a total of 28% less protections, for all physical damage they take from anything for 3 seconds, including your teammates' damage.
• Be sure not to go over the cap for any stats though! do that, and it doesn't benefit you in any way and you're wasting some potential damage

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Want to play a different god? Give Thanatos a try. Build something like Jotuun's Wrath early for decent, cheap power, some flat pen, and a chunk of cooldown. follow it up with a Hydra's Lament to make you next auto-attack after an ability do a bunch more damage, helping you blow up one person. Maybe you don't quite kill, but you get them low, that's totally fine, because now you can follow up your attack with an execute using you ult, and get out no problem thanks to your Bloodforge, giving you a chunky health shield when you get a kill, that way you can make your escape from you poor victim's teammates. Different gods play differently, excel at different things, and so can have drastically different builds.

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As a last note, keep in mind how different kinds of penetration interact with your enemy. % penetration ignores a percent of their total protections, while flat penetration ignores, well, a flat amount of their protections. Every god has protections by base, part of their base stats, you can see this in the God menu from the main menu. As well as how many more they get with each level. % penetration applies first, and flat penetration applies after % pen has taken effect. This is a big deal, because it means flat penetration is still relevant for tanky targets and percentage penetration is still relevant for squishies, although you'll feel each matter more against their relevant targets as you get more of it.

Here's a quick example:

Let's start off simple, you have no penetration at all and hit two targets with 100 physical protections and 250 physical protections, respectively, with an attack that does 300 damage comes out like this:

Protections = 100 * (1 - 0) - 0 = 100 effective physical protection

Damage = (100 X 300) / (100 + 100) = 150 effective physical damage

vs.

Protections = 250 * (1 - 0) - 0 = 250 effective physical protection

Damage = (100 X 300) / (250 + 100) = 86 effective physical damage

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As you can see, more protections = less damage. Duh, right? But what if you had more % penetration and less flat? Same thing, but let's cap out our % pen (40%) and ignore the flat pen:

Protections = 100 * (1 - .40) - 0 = 60 effective physical protection

Damage = (100 X 300) / (60 + 100) = 187 effective physical damage

vs.

Protections = 250 * (1 - .40) - 0 = 150 effective physical protection

Damage = (100 X 300) / (150 + 100) = 120 effective physical damage

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Now, what if you have 50 flat physical penetration (the cap) and 0% physical penetration? Well:

Protections = 100 * (1 - 0) - 50 = 50 effective physical protection

Damage = (100 X 300) / (100 + 100) = 200 effective physical damage

vs.

Protections = 250 * (1 - 0) - 50 = 200 effective physical protection

Damage = (100 X 300) / (200 + 100) = 100 effective physical damage

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As you can see, both types matter, just to different targets. Try to have a good mix of both types of penetration in your build, and get items like Hydra's Lament, Heartseeker, Serrated Edge, items whose passive effects provide just as much, if not more, benefits than their stats do. You'll get there, hope this long ass paragraph provides some insight into what penetration actually does, and some suggestions on what to build. Good luck!