The only one I find all my characters using is the first one in Restoration, to halve the cost of healing. Just about any character needs to heal, and we all get the spell to use, If they have to heal a lot, then we'll pick the Regeneration perk to make it more effective.
All the others are specific to the build, although it seems that a character that doesn't smith and enchant for themselves is going to do so for their follower, so those two trees will see some use in most games. Not all, as some play solo.
I've never used the dual-casting perks. The cost/benefit of that doesn't strike me as worthwhile. The same amount of magicka does more damage if I don't dual-cast.
Alchemy is a soak for spare perks in the early game when the boost to selling prices helps. Later on, money isn't an issue, and only characters that are actively using potions will bother.
I've used Eagle Eye, but usually don't bother. Steady Hand seems a waste. A stealthy archer has all the time they need. The Bullseye perk is never used (after the one game where I found out it's worse than useless).