So, thoughts on the ending?
I chose...destroying the Reapers.
Seems to me nonsensical that they are "agents of order" when they're basically big scary zombie dudes. Babylon 5 did it better, where the Vorlons were Angels and the Shadows were scary spiders -- but that's because the Vorlons had altered the races to perceive them as such. It makes not much sense for the Reapers to scare people so much.
Because Bioware relies waayyyy too much on zombie enemies. The Reapers aren't really any different from the bad guys in the Dragon Age games, down to creating their own evil versions of the good guys and not really explaining all that well why they're doing what they are. They're essentially galactic cockroaches, just like the Dragon Age bad guys.
Overall, I have to give the series a big meh.
KOTOR and Jade Empire were superior games. More thoughtful and better stories.
Sovereign states way back in the first Mass Effect the Reapers set up the galaxy with the mass relays, the Citadel, and various bits of element zero-based technology so that civilizations would develop technology along predictable paths to make them easier for the Reapers to "harvest". But really there's no old legends or stories about the Reapers that make people scared, it's just fact that the Reapers will tear through each faction's fleets like so much tissue paper that makes them scary (to the people in-universe).
The Reapers may employ "zombie" ground troops, but they aren't "zombie dudes" themselves. They're more like eldtritch Cthulu-esque science fiction monstrosities. Their goal is made pretty clear by the end -- they have observed a pattern where "the created always rebel against their creators" so they reset the galaxy by wiping out all advanced life every 50,000 years or so. That may sound a bit stupid, and indeed it is fundamentally flawed. But there's a point I don't think they ever state which I think would make a bit more sense -- they periodically wipe out advanced life to prevent some life from arising with the capability to wipe out
all life and no inhibitions from doing so. They justify wiping out races by creating Reapers out of the races' genetic materials, thus "preserving" them.
I will admit that the Reaper ground forces aren't all that original; they're just a spin on the "mutant zombie army" that's been done before, as you said, in Dragon Age, but also in Halo with the Flood. Banshees are still pretty damn freaky, though. Cerberus from a design standpoint are just some standard human bad guys. The geth spice things up a bit -- the most creative geth unit was actually the geth "hopper" which stuck to walls, but it only appeared in the first Mass Effect. I sort of wish the Collectors had made an appearance in Mass Effect 3; they apparently were used by the Reapers in the war, as they are referred to in Codex entries about battles and were later added as an enemy faction in Mass Effect 3's multiplayer.
I haven't played Jade Empire, but I will say that I prefer the Mass Effect series on whole over the first Knights of the Old Republic. You simply have more time to get emotionally invested in the characters -- HK-47 is great and all, but Mass Effect has Garrus, Wrex, Tali, Mordin, etc., etc. The antagonists in Mass Effect are better; Saren is a bit more of a complex villain than Darth Malak, and the Illusive Man is even more so. There are better suspenseful or emotional moments in Mass Effect, particularly in the third.
Also, while Knights of the Old Republic was a great game, I wouldn't call it particularly "thoughtful". It was great because it managed to nail down the classic Star Wars feel and story, and did a good job of developing interesting and likeable characters. But did it do anything truly thoughtful with its themes and messages? No, I don't think it did. I'd say the
second Knights of the Old Republic was actually thoughtful, with its speculation on the role of the Jedi, how the galaxy regards the Jedi, what is a Jedi without the Force, what the real difference between the Sith and Jedi is (if there is any), and it didn't resort to cliché answers to any of that.