Maybe this is obvious, but maybe it's not: all gear and subclasses level up their individual skill trees only when they are equipped. So, if you are trying to level a specific piece of gear to unlock a bonus, or get to a specific skill on a subclass, you better be actively using it... or make sure you have it equipped when turning in bounties, finishing quests, etc. Doing the latter can help you level gear that might pull down your light level otherwise, if it gets bonus damage or defense as part of its leveling progression. Individual skill tree perks need to be activated by selecting (and, often for gear, "purchased" with various in-game currencies) them on the skill tree for that item.
On armor, spec to certain play styles based on the intellect (super use cooldown), discipline (grenade use cooldown), and strength (melee cooldown) ratings that it has. If you are a grenade-tossing machine, get that strength up, son. If you dig on supers, go with intellect. Sometimes it's worth the small light level hit you might get by using an item with lower defense rating if it has a higher attribute rating for your preferred play style. Many pieces of gear now have dual attribute bonuses (e.g. intellect and strength), but they usually have less of each than a piece that has just one attribute bonus. If you hover over the icons for the attributes (just to the left of your defensive gear icons on the character menu), it will tell you what your current cooldown for skills is based on the attribute bonus. There are tiers for the cooldowns, so small increases in the attribute bonus levels may not result in an actual reduction on the cooldown. Sometimes you'll get a piece of gear that has a higher defensive rating but lower attribute bonus than one you're already using. It's worth equipping it, though, to see if your light goes up and your skill cooldown stays the same.
Don't be afraid to scrap stuff if you don't like it or it's under-leveled and pulls your light level down. You'll get stuff (e.g. weapon parts) that is needed to do many of the upgrades in gear skill trees. These are the in-game currencies I previously mentioned. That said, if you have a piece of gear that can help pull your light level up, but doesn't align with your likes or skill spec, keep it around to do the Cryptarch Engram decoding trick previously described. That will help you get higher quality gear from decodes.
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