I've found this to be one of my biggest issues having played through many times as well.
I haven't finished Gale or Wyll's routes, and that's primarily because of the reliance on long rests. Couple reasons why the long rest reliance is so frustrating IMO:
a) If you don't go looking for the information, there's no way to know that you have to rest a certain number of times for certain relationship items to advance. I've romanced every other character but Wyll and Gale because they didn't have as much reliance on this.
b) It's easy to go without resting as much as needed to trigger these events via natural playthrough. If left to my own devices (no reliance on long rests for dialogue), I'd only long rest 3-5 times during the current early access playthrough. I mean, the very basis of the story discourages you from long resting, since normally you'd become an Illithid within 7 days.
c) Needing to long rest actually detracts from the fun of the game if you like some difficulty. I am not used to D&D being a game where I get all my spell slots and special moves back after EVERY fight in a super dangerous situation. It makes the combat very easy and boring for a seasoned player.
I love the idea of tying the dialogue to short and long rests.
It would really incentivize players to care about the short rests, and not find them as just boring easy heals for the majority of classes that don't benefit greatly from them. I think it would also give more gravitas and appeal to the sense of time in the game.
A short rest in 5e is supposed to take an hour, it's not supposed to be so brief as to be worth ignoring completely. If a short rest could trigger a "freeze" or something to the rest of the world, so you don't get interrupted with battles or outside dialogue for a few minutes while you do the short rest, that would work.