About the HM thing... It'll be the same as in 3rd gen. HM's cannot be given to pokemon->traded. So they could make a HM9 Whirlpool if they want to.
Is flash useful anywhere in Sinnoh? I don't remember any area I used it. If it's not, then I have to say that it's a kickass tm, which everyone teaches to a pokemon as fast as they can, looking at what a great move it is.
About apricorns...
They probably won't be in the remake for different reasons:
1. Gen III completely renewed the berry concept.
2. The Pokeballs you get from apricorns have got replacements in form of more useful pokeballs in the 3rd and 4th gen:
Level ball-Nest ball
Lure ball-Net ball
Fast ball-Quick ball
Moon ball-Dusk ball
Friend ball-Luxury ball
Heavy ball-Timer ball (this is a bit wacky Dx)
Love ball-Heal ball (and that even more......but still seem more similar than compared to effects of other pokeballs)
3. They are not programmed in DPP!
But seeing as every apricorn ball has it's upgraded version, those could be made from apricorns instead. There would just have to be something that prevents you from trading them. For that they should not be giveable to pokemon. So all that would have to be done is a key item (apricorn bag or whatever)for storing apricorns, working like the pokeblock case.
So the only problem I see right now is the absence of the berserker gene in DP....anyone remember any other items which are not key items?