Why would you join Malak? You do have the option to team up with Bastilla and kill Malak and rule instead of him. I don't see why someone that would go the dark side route would actually consider joining with someone that already betrayed them. But then again, that goes along with the "Rule of 2" thing where it seems like the apprentice is supposed to overthrow the master at some point.
Thing is, this was ignored by the sequel by neccesity.
One thing people must keep in mind is that, for there to be a continuity between games, it's impossible to have a wide variety of setting-destroying choices. Branching paths are all well and good, but at some point the devs cannot create two entirely different games based on whenever you sided with the villain, and then two OTHER games in the second sequel, ad nauseum. In every single RPG that had major choices like that, the sequel had to impose a canon
Examples? here we go: Baldur's Gate 2 forced a continuity on you, you always had a party of goody two shoes with you. Fallout 2, your character always ended up saving Shady Sands, using guns, recruiting Dogmeat and settling in Arroyo, despite there being a bad ending to that game. KOTOR 2, Revan was always a mastermind who didn't much care about good and evil and didn't stay as Sith Lord. Witcher 2 you always romanced Triss and your choices in Witcher 1 were basically irrelevant. Fallout New Vegas had NCR and the Brotherhood still exist no matter what you did in FO2. Have I missed any?
Now, for these games this is well and good, since save import is not a big deal. But with Mass Effet before, and with Dragon Age now, save import is a Big Deal. People want nitty gritty details, they want their own continuity, or Bioware wouldn't have bothered with the Keep. And realistically, it would be very, very hard for Bioware to allow something like the Inquisition taking over the Chantry without needing a ridiculous number of plot flags in the eventual fourth game, let alone things like siding with Corypheus for whatever stupid reason. Or, you allow those options and don't allow them importing. Which will ****** people just as much if not more.
I do agree that it's a shame that lolevil options aren't available (even if I personally never took them). But realistically, you either get less dramatic worldstate variations, or no serious save import. Bioware chose the former.
I can still play the style of character I personally want (moderate Andrastian mage, pragmatic and blunt atheist, anti-mage Qunari, polite but pro-mage and anti-chantry Dalish), so honestly as far as role-playing purposes Inquisition has me covered like, well, no other Dragon Age game honestly. I can decide the outcome of the Mage-Templar war, the Orlesian Civil War, and greatly influence the future of the Chantry. My Inquisitors more than make their marks on the world. It's a shame that I can't deviate even more, but well, I also realise I can't have my cake (solid save imports) and eat it too (mwahahaha evil options).