A few people asked earlier in the thread what changes you can make. Unlike in DA:O you'll see direct results when finishing a side quest.
Hinterlands - Eradicating the rogue templars and mages and erecting watch posts brings peace to the region.
Fallow Mire - No real change aside from closing the rifts.
Storm Coast - Eradicate or recruit the Blades of Hessarian to bring peace to the region.
Forbidden Oasis - Save your soldiers and disrupt the Almari presence. There's not a lot of change that happens here since the villages were hit with plague months before you arrive.
Crestwood - Deal with the open rifts, undead and bandits to bring peace to the region.
The Western Approach - Eradicate the Venatori and deal with the Wardens to establish a military presence here.
The Exalted Plans - ???
Emerald Graves - ???
Emprise du Lion - Eradicate the Red Templars to bring peace to the region.
The Hissing Wastes - ???
I either didn't bother with those areas or don't have an accurate recollection of exactly what happens there.
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Decisions that are reflected in the ending:
- Choice between recruiting either the templars/mages
- Banishment/recruitment of the Wardens
- Hawke or Stroud/Loghain/Alistair in the Fade
- Who rules Orlais
- Who is Divine
I had Morrigan drink from the well so, I don't recall if that's mentioned again.