Wow, gameplay is completely different so this will be entirely subjective, but okay.
(1) Story/lore
Both are great. Mass Effect is straight sci-fi, whereas AC is time travel sci-fi/conspiracy theory/historical. While I appreciate the codex in AC more because it's grounded in the actual world we live in, ME is easier to follow, with one central protagonist and direct sequels. ME wins for me.
(2) Technical
Played all three parts on 360 and imho it's a marvel what they did with the hardware. At the time the first game came out at least I couldn't believe the detail in the characters. Also, ME2 and 3 hardly miss the 30 fps mark. AC... lol. On PC they run at 60 fps, on PS3 AC3 runs like a complete turkey. ME wins.
Oh, I'm not going to bother. I think they are both great series, and in an era where mutliplayer has gone mad, I like that these studios have taken the effort to construct rich universes with deep singleplayer campaigns. Yes, they are blockbusters and not the height of literature, but I find the story telling experience to be more compelling than the latest Hollywood popcorn movies.
Edit: I should have added that I Youtubed Revelations because they dragged Ezio's story on for one game too many in my eyes. I still respect AC but annual installments of the same thing were too much.