I completely agree that the companion presets are handled terribly. That's why I bit the bullet and installed the Fort Joy mirror mod. It makes things that much less frustrating early on, and it's up to you to abuse it for constant re-specs, or just use it that once (per companion) to fix those horrid presets.
While I can sort of live with the less-than-stellar attribute disposition of some presets (Int on a Conjurer that is expected to do physical damage in my party setup is kinda useless...) until getting to the Lady Vengeance, messed-up civil skills and/or talents are a constant major pain in the nether regions from the get go. Need a thief? Shadowblade is literally the only "choice" you have. What, you want a full magic damage party? Sucks to be you. You want a buddy for LW who can do the talk-to-Buddy shtick? Wayfarer or Conjurer, and that's it.
In a game with this much potential for individualization, that is just not good enough.
Easy solution, after choosing your companions combat role, add two more pages of dialogue:
1) "I'm also very versatile outside of combat. What do you want me to focus on?"
- Trade
- Diplomacy
- Lore
- Crime
- etc.
2) "I'm quite a talented fellow/gal. Do you want me to do what I do best, or do you need something specific?"
- Do what you do best (talent that befits the combat role, like now)
- Pet Pal
- Lone Wolf
That would deal with the bulk of the preset problems, and still be simple enough for new players to understand.
