Which perks have you come across that are still not working?
My bad, i just did a fast research and it seems most of them got fixed with the last patches. I haven't played in a long time, so i didn't test again the old not-working perks recently.
Still, there are perks still useless to this day (the Commando perk, since there are not enemies to be found near water), or in need of rebalancing (the Dagger Dealer perk for example, since you can't pick up thrown knives from corpses).
Stronger Together is rarely useful, PLUS you need the Trasporter perk too for it to work. This means you have to spend TWO freaking points on a perk that is hardly worth it.
The Grenadier perk is redundant, since we already have the Explosive Analysis ocular mod.
Anything that adds damage, or has anything to do with mechs and robot, is unnecessary, since mech encounters are few and far between. Maybe in future with expansions...?
Generally speaking, many perks are boring, irrelevant buffs that hardly make a difference in combat. I'm not saying they all suck (the Cool Blood skill tree is fun once you invest a reasonable amount of points in it, for example), but many doesn't really enhance the experience in any substantial way.