I've heard it suggested by many of my fellow gamers that you can have good gameplay or a good story, but if you try to cram them into the same experience you just cripple the effectiveness of both. Perhaps you agree? Perhaps this is part of why you don't like the ending of the Mass Effect story?
Yet this uses a very narrow definition of narrative. "Story" and "plot" are often used interchangeably, but in a literary context, the two are distinctly defined.
Respected literary critic Robert Scholes describes "story" as the raw materials of narrative: the basic sequence of events in chronological order. "Plot" is the refinement of those materials, "ordered so as to engage the emotions and develop the theme." Story is the overall content: plot is the diegetic structure.
Once separated, they can be individually applied to video games. "Plot" is the narrative woven into a game by the creators: it's Cole Phelps' rise through the ranks of the LAPD or Ethan Mars' desperate search for his son. These narratives are often entertaining in a conventional sense, but a plot is carefully constructed and allowing players to get their clumsy hands all over it may diminish its effectiveness. The player's actions sometimes have to be controlled to keep a plot dramatically satisfying.
Gamers are used to having their control restricted occasionally: cutscenes convey important information, while keeping players from wandering off or trying to kill important characters. How many times, playing GTA San Andreas, did you want to just want to blow away Samuel L. Jackson's Officer Frank Tenpenny... no, how many times could you think of a better way of dealing with him than Carl Johnson had thought of, but couldn't because that's not where the plot of the narrative, was going?
Other times, it's better to let them wander off. An engaging plot isn't everything and when players are let loose, "story" is born. Stories in games aren't finely crafted, but we enjoy them in other ways.
The plot of Just Cause 2 is something about toppling a corrupt dictator, but I'll remember it for the stories I created: like the time I tied a boat to a helicopter. Giving players the tools and the freedom to create their own stories is perhaps the best thing games can do with narrative. EVE Online, for example, has no plot, but it has more stories than you could possibly count.
In my first sessions on EVE I ventured into low-sec space to mine some particularly hard-to-find Jaspet ore. I got jumped just before my cargo hold was full, and warp scrambled before I could jump to the stargate I was already aligned to. A few rounds from the enemy battleship and my teeny little mining frigate and the valuable contents of my cargo bay (which I'd just spent quality time digging out of the asteroids) were turned to dust, and I was floating there in my capsule, a helpless, insignificant noob in a galaxy with far more going on at that one time than just my little story. I begged my assailant to let me escape in my capsule, but he'd already scrammed that too... I was podded before I'd already hit enter to send the "f*** you, a-hole" message I had prepared.
Honestly, it wasn't a "fun" experience at the time, but looking back, I can appreciate it as a narrative. It's not a timeless classic, but it matters to me because it happened to me. As game academic Chris Crawford wrote of the gamer in general, "the story he creates is his special story...no other story will ever be the same. Because it's his special story, it means more and has more emotional power than any high-tech Hollywood extravaganza."
I'd argue that there is no conflict: good gameplay begets good stories. And your story on Mass Effect is not determined just by the quality of the ending, but the meaning you take from the stories you are a part of yourself.