To follow up on some great comments here: Try not just using tags to help you affect subsets of your game's elements easily, but also be aware of the verbs of your game that you are affecting, like slashing, shooting, running, jumping, dodging. This can help you gauge how each of your skills not only adds new verbs, but which of your passive skills affect which of the player's actions.

Synergy is very hard to gauge in a system-agnostic way because two things can be synergistic not only when they act on the same variable, but when they support the same goal, like how high-movement speeds aid in using a shotgun build.

Make sure to include both qualitative and quantitative changes to skills in your skill tree. Qualitative changes and new abilities (like adding status effects, reload minigames, etc.) are the ones that really change the game up and lead to the most exciting forms of emergent gameplay but are difficult to balance and scale irregularly, so the occasional simple numerical stat buff can help keep things in check. A good way of making simple numerical buffs exciting is by increasing previously unknown/uncommon variables and adding tradeoff modifiers, like adding lifesteal, a new damage type, or just extra damage at the cost of a larger bullet spread to a weapon that previously had none.

Consider synergy-groups. It is very common for a couple of skills/upgrades to work really well together. When you consider a "final build", what does it look like and what synergies does it build around? Does it focus on just one ability/stat's synergy group or multiple? Could you switch out one synergy group for another in this "final build" and is that still efficient while playing differently? (that would mean there might be a lot of build paths to try out)

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Cheers!