For me, it's actually that the nudity added an undertone and ambiance that I think a clothed scene would have lacked.
Afraid I don't see it.
I'm not saying that you're asking Bioware to make the game E for Everyone Iakus, I'm saying that you might be better off doing so than asking for the multiple workarounds that would be required for you to turn ME:A into a bespoke game of your very own.
Workarounds Bioware has done before. In the Mass Effect setting, no less! And without me to ask for them!
And on the flip side, I don't understand why the DAI scenes bothered you. I get that it's a fact, but that's it.
While we could work on our mutual understanding, what use would that be? Even if you understood my feelings, and I understood yours, our tastes wouldn't change. We'd still be right here.
Yup, I'd be right here, saying if you like nudity, that's fine, just provide an alternate path to let people avoid and/or skip past it.
Because this is a game about choices
But why should Bioware not use an important set piece? Nudity after all has artistic value - particularly with the connections to vulnerability that obviously exist.
Yeah, well, I've had people tell me RGB has "artistic value" but I don't see that either. 
I'd still rather have alternatives.
This, to me, makes all the difference. I've watched the no-sex version of Dorian's romance scene and played the regular version and, to me, the nude version has so much more impact. Not because we get to see someone's toned ass but because the nudity emphasizes Dorian's vulnerability. There's a level of trust in being in a position like that with someone and, based on what people have described for Cassandra's romance, it's similar. Stripping away the armor and the defenses and exposing the person underneath--the impact is much more effective with the nudity than it is without, IMO.
Likewise, with characters like Bull and Sera, Isabella or Leliana in DAO, for instance--these characters are earthy, sensual people. Leaving them clothed or skipping nude scenes with them would seem forced and bit silly in the context. Even if the relationship development or character development doesn't benefit from the nudity, the fact that they are such sexual creatures would make a lack of nudity in a sex scene seem almost like we should be ashamed of the act which is the complete opposite of their characters. Now for characters like Cullen and Josephine (I haven't played either so know little of how they played out), I could see using limited nudity or none, limited or no scenes of an obvious sexual nature or fading to black and leaving it up to your imagination because it would fit their characters a bit better.
In addition to the characters, though, the settings should play a part in how mature they make scenes like this. If the setting was a 1950's world or a Victorian world where seeing a woman's ankle might be considered scandalous, I could see avoiding nudity in keeping with the atmosphere. But in ME we're talking about a future galaxy with multiple cultures and various attitudes about sex and no discernible examples of prudity. It's immersion breaking, IMO, if you set up a galaxy that seems sophisticated and unfettered with too many sexual inhibitions and then turn around and make it seem shameful to watch a romantic scene with obvious sexual overtones and nudity by fading to black while they're clothed and then picking things back up again with them fully clothed or doing the clothes humping thing that was so ridiculous.
I have not seen the Dorian nude scene, but I have seen the Cassandra one. ANd really, the only thing it adds to the dialogue is nipples. She could have been wearing a sheet, a robe, or even be fully dressed (or even clever camera angles), and it wouldn't have changed the scene. It could have been done bring one of the make-out sessions above the smithy, and it would have been just as impactful to me.
Also, you can decline sex with Leliana in DAO. She may be worldly, but she's also pretty considerate 
Why, oh, why does not wanting to watch a nude scene ALWAYS SEEM TO COME BACK TO "You just want underwear sex to return"? Seriously, Why? It's really getting frustrating. It's like talking to a wall.
Again, it's NOT ABOUT SHAME!!!! It's about CHOICES!!!