I would love to see more interesting, gameplay changing perks, or a flaw system where you do not get a perk point but some tradeoff, for example:
Go Slow, Reach Farther: If time is money you are rich. You cannot sprint anymore, but you walking speed is increased by 25%.
Nerves of Glass: Spacer's Choice developed a neuro optical implant allowing for fast reflexes, unfortunately the glass wires can break easily. TTD time increased by 100%, health decreased by 50%.
Far Sighted: +50% damage at distances above 15 meters, -50% damage below 5 meters.
Space Ninja: You get 40points in sneak, but only when your carry weight is below 50kg.
Wisdom of Elderly: Thanks to your old age, you are more experienced (gain 3 levels immediately), but also frail (movement speed -25%, can wear light armor only).
Fight Through the Pain : You do +50% damage against enemies, but 5% of that hurts you instead.
etc.
This combined flaw / perk solution would be more immersion friendly. Right now many perks seem to be by the numbers, and having a flaw right permanently crippled does not seem to worth the to accept with the current perks.
Companion perks (with the exception of the highlighted ones, have nothing to do with the companion's skill or personality, and thus are not so interesting.
Summary: Please make perks interesting. Thanks.