In my personal opinion there have been many changes over the course of the games & I do find DA:O to be the darkest, mostly on the side of player choice, but also from story telling and actions too.
2 examples I like to use when telling friends about DA:O are:
1: During the Dalish origin story (never tried it with the others) if you repeatedly refuse Duncan (as I still believe you weren't sick) he'll turn around and tell you that he'll "drag you to Ostegar kicking & screaming." Yes when he's in the company of nobles he's completely different, to me (& I've not read any of the EU material) I get the impression that Duncan has a darker side, that if forced will show itself, despite the fact he tried to portray himself as the 'noble' knight.
2: Redcliffe or to be more accurate, ignoring Redcliffe, as doing so is just a really shitty thing to do, as you're going there specifically to see Arl Eamon & have to come back anyway.
In DA2 there are still some dark choices of dialogue to make, but less on actual outcome, for example, if I remember correctly, you can tell Anders that you agree with him & would have supported his decision to blow up the chantry. It's been a while since I played DA2 & didn't go through it as many times as DA:O, so cannot really think of many more examples...oh wait, you can kill Merrill, but I think you need high rivalry & to side with the templars, never did that myself, so don't know for sure.
Inquisition: For the most part I was glad to be back in the 'driving seat' of the narrative, but certain things stuck in my throat, like; why could a mage-quisitor only use tranquility as a punishment? To me it made no sense, but that's not all. I was pleased that you could play a character that didn't believe they were the 'chosen one' but annoyed that it only centered around Andraste. Why couldn't Lavellan say that she didn't believe that she was sent by the maker, but she was by one of the creators?
Something I would have like in the game would in my opinion have really added punch would be the option to disband the chantry entirely, but you're left with the undertone narrative that Andrasteism is the religion, further accented by the dlc's.
Which leads me onto the next point, nobody questions events anymore, how do we know that what Solas is saying is 100% true? Yes there are messages in the Elve ruins in Trespasser, but they are his ruins, why not throw in the chance to question, to show your own interpenetration of events? Simply because 'he said so' doesn't really make sense.
Ok, gone off topic a little there, but yes, I feel Inquisition, while an enjoyable game, really missed putting the darkness of choice back in the players hand & going to close by saying, would have loved the choice to have played Envy's inquisition.
Just my opinion.