I already said that DA:I is irrelevant here. All those plots could have been created during DA:I's development once Bioware was already in bed with the red lyrium idea.
All right, then let me rephrase that: the devs have said that while individual details and quests change a lot from early conception to final development, the overall "spirit" of the story and progression of events stays the same.
For example, early DAO drafts were going to reveal that Eamon and Cailan were plotting to divorce Anora to remarry Celene. Loghain caught wind of it, fought with Cailan about it (which Cailan's tent guard at Ostagar hints at in the final cut), then when Cailan refused to yield Loghain left him to die at Ostagar, took over as regent, and launched his own Orlesian witch hunt. The Warden was going to uncover this over the game, ultimately culminating in Celene appearing at the Landsmeet to reveal to vindicate Loghain's Orlesian paranoia. Most of this got cut; the plot is only hinted at in a few letters found in the Return to Ostagar DLC (with Loghain lying about not knowing Eamon's and Cailan's plan beforehand), and Gaider changing his mind that, "Loghain knew about it, and was planning on talking to Cailan about it after Ostagar but then felt forced to leave him behind after the signal was lit too late" BS.
Similarly, many new revelations of elves in DAI that were supposed to be revealed in DA2 but got hoisted over to DAI. The Exalted March DLC was intended for DA2, but got cut. Rather than scrapping the ideas though, they simply moved the story ideas into DAI. For example, The Temple of Mythal was originally supposed to appear in the Exalted March DLC which Hawke and co. discovered, but instead it wound up appearing in DAI where the Inquisitor and co. discovered it. The devs have specifically said that the revelation that vallaslin were slave-markings and that Arlathan fell to civil war rather than Tevinter was planned from the very beginning; it wasn't just something they retconned or made up for DAI. Apparently also the revelations of ancient elves being not-so-nice, the Temple of Mythal still standing, ancient elves still being around (Abelas and co.), and ancient elven gods manipulating world events behind the scenes (Mythal and Fen'Harel) seems like it was all planned from the beginning. Even though the information that was meant to be presented in a DA2 DLC wound up being presented in a DAI main story quest in a very different way, the core information and series of events (the revelations that ancient elves both weren't that nice and are still around and are manipulating world events for a comeback) stayed the same.
The devs have said they've got the basic, overall main story for the first five DA games all planned out. We're only on Game Three of a Five Game Series. A lot of ideas that were supposed to appear in one form but ended up appearing in another form (Cailan's planned divorce of Anora for Celene) or moving to a different game altogether (Temple of Mythal from DA2 DLC to DAI main story) and the overall story largely playing out the same regardless of player choices (the Warden stopping the Fifth Blight, the Mage/Templars breaking out into open war by the end of DA2, the Mage/Templar War being stopped and the Circles being restored and the College of Enchanters being built by the end of DAI, etc) makes me think some poorly executed features in one game that wind up playing a huge part in another means it's supposed to be important from the start.
THAT'S why I think red lyrium was supposed to be a major player from the beginning. Regardless of whether you think red lyium turning out to be responsible for Meredith's tyranny and insanity being a last-minute ass-pull at the end of the game, the fact that it is such a huge player in the overall DA2 story arc and continues into the DAI story arc makes me think it was supposed to be there from the start. It certainly helps that revelations about red lyium in DA2 turn out to be really lore-heavy; Varric sends Bianca to learn more about it, she accidentally gives Corypheus the means to use it for some major DAI enemies, she discovers that red lyium is blighted lyrium, and since it's blighted that means lyrium's alive, then the Inquisitor discovers in the Descent DLC that lyrium is the blood of Titans, and there have been hints in DAI that the titans and/or the dwarves' connection to titans will play a much bigger role later.
I think it's more likely that red lyium was supposed to have more buildup and integration into the plot, but since the stupid game was rushed to release, they couldn't give it the time and attention it deserved. Since they had to rush this stupid game out the door by a quick deadline, it's like, "Okay, just hit the important points; Hawke and Varric find it in the Deep Roads, Bartrand brings it to the surface, it slowly drives Bartrand mad, Hawke and Varric relieve him of it, Meredith eventually gets her hands on it, it slowly fuels her paranoia and insanity, it pushes the mage/Templar conflict to the forefront. Okay: Boom. Done. Animate it and push it out the door."
Saying "Well, don't bring DAI into this, only judge DA2" doesn't really work because a lot of the overall narrative progression covers multiple games. A seemingly innocent little detail in one game can turn out to be a big story point in another; and the fact that red lyium plays such a huge roll behind the scenes this game, and turns out to have a big roll next game, and ends up revealing fundamental lore about this universe next universe (Titans being underground, lyium being their blood, and dwarves having some mysterious connection to them) makes me think it was always supposed to be there, it was just badly presented this game.