Honestly, I wouldn't call the Mass Effect 3 ending "bad". It does lack any real sense of closure, and quite literally pulls a Deus ex machine out of nowhere in the last 10 minutes, but the endings CAN stand on their own, and if viewed with a certain mindset, can be serviceable as endings to the game. Personally, I'm not a fan of them, but I wouldn't consider them "bad", just extremely unsatisfying and anti-climactic. Especially to me, and others, who had grown quite attached to the setting.
If you want to talk bad endings, I can toss a couple into the hat. There will be spoilers
Chrono Cross
We get an ending that feels tacked-on, for no other purpose than to make a minor, fairly half-assed link to the game's much better prequel. The final battle is against the last remnants of the big-bad from the original Chrono Trigger, except it is a gimmicky, and sometimes frustrating, puzzle-fight. The ending itself didn't make a lot of sense to me, and the character claiming to be someone from the first game did not even look like the old sprite.
Honestly, if that whole final Time-Devourer sequence would have been cut out, along with the attempts to link itself directly to Chrono Trigger, Cross could have been a fine stand-alone/spin-off game.
Xenosaga
Six games worth of ideas crammed into three. The final game is a mess, with characters making referrences to events that happened in a whole other game that had to be cut out to shrink the series down to three games. The ending has no real sense of closure and the big explanation for what the gnosis (important recurring enemies throughout the series) are was just stupid. The main villain's motivation was kind of neat though...although, it did follow some very circular logic. "The universe will eventually be destroyed in billions of years. I shall destroy the universe to reset it so that it won't be destroyed".
Drakengard
I have never seen a game that hated its player as much as Drakengard did. Every one of its endings involved some kind of Twilight Zone twist, and were generally unsatisfying (...much like the entire game turned out to be by the end). There's also the secret ending, which takes hours to unlock by finding ALL 100+ of the game's hidden weapons (some of which are literally impossible to find without a guide's help). All you get is a mindfuck of an ending involving gigantic flesh-eating space-babies from another dimension, a 1000ft tall pregnant space-woman who gives birth to them, a final battle that draws you and your talking, fire-breathing dragon into modern-day Tokyo to challenge the pregnant eldritch space-momma to a rhythm game...which, if you win, just ends up with your character getting blown out of the air by a sidewider missile from a jet. The final image of the secret ending is of your dead dragon impaled on Tokyo tower, bleeding and with huge chunks blown off by the missile.
Drakengard is kind of beautiful in that way though. It is a game that hates being played, and hates you, the player, for trying. lol
Valkyrie Profile 2: Silmeria
Okay, I loved the original Valkyrie Profile. It was one of my favorite games on the PS1. The sequel is largely bland but unoffensive until the very end when time-travel is invoked out of nowhere. The series of events that the time-travel results in kills off several of the first-game's main characters, including Lenneth (the main character of the first game) who had come back in time to try and help. It also changes history to the point where the first game's plot would be impossible to happen, effectively nullifying the first Valkyrie Profile.
I imagine there are other endings I really thought were bad over the years... but these are the ones that initially come to mind. My personal worst game endings. Mass Effect 3 is nowhere near then in terms of horribleness, lol. It ain't good, but it isn't VP2 or Drakengard.
