I disagree with two of your hero pairing Jin/Bart and Jr./Billy. The last one especially seems to me that you just made the two gun wielders duke it out. :p
Alright Villains:
Wilhelm and Minag
Why they were paired - They are the game main antagonists and manipulators, their origins and natures are also the same. Miang really is the cause of all the issues in Gears much like Wilhelm is for Saga. Krelian is there but he's doing his own thing and it still only works if Miang's plan comes to fruition as well, he just added a final phase that isn't part of Miang's programming.
Both Miang and Wilhelm are non-human beings hiding within humanity to manipulate history and allow some terrible events to unfold for the sake of a goal that spans thousands of years. Neither character is truly evil or good, they are simply accomplishing a goal. Miang gets the more villainous light because her plan involves resurrecting a self aware. terraforming anti-planetary weapon system, whereas Wilhelm is simply trying to prevent human conscious from making the realm of real numbers (material world) collapse and take the world of imaginary numbers (God realm) with it by making the universe reset before it reaches a point of no return. Yet the point I'll make is that both characters are largely indifferent to their goals beyond getting them accomplished. Wilhelm is not saving the world because he feels for humanity, nor is Miang trying to end the world because she's some evil meglomaniac. They are both simply constructs fulfilling the purpose they were created for and they both do an excellent job. Granted certrain facors put a wrench in Wilhelm's plan whereas Miang ultimately succeeds in her goal (Hey its not her fault some heroes came and kicked Deus' ass after it finally got restored, her job was just to get it running again not keep it alive.). For me, Miang wins this because... well frankly I don't understand what any of you see in Wilhelm, he spends the first two game ssitting smuggly in his office clasping his hands while doing his best Mr. Burn's impressions while saying "Excellent it's all going according to plan" By the time he finally emerges as the main antagonist, I feel he's been completely overshadowed by the far more colorful Albedo and sinister Yuriev. Wilhelm flat out has no real character development and I felt his finally entering the stage was met with less "Awe" and more "About damn time". Minag to me was better because as Forsaken Lover points out, when she first appears, you don;t really expect much from her, and then as the plot goes on you see she has connections with some unsavory people but the player is still in the dark about them as well so you still don't assume her actual role and then finally it all begins to come together and you realize she really is the big manipulator and unlike Wilhelm whose big revelation was that he was the leader of ever organization in the Saga universe, Miang does all while being the most unassuming figure. Miang was a a bit of a surprise, more than Wilhelm's whose introduction and initial role in the story made it obvious he was going to be really important.
Winner: Miang
Krelian Vs Yuriev
Why are they paired - Both characters are normal people who through terrible circumstances, discover the true nature of the world and its grand conspiracy and then both try to manipulate events to pull off their own solutions. Yuriev is trying to destroy U-DO, because he mistakenly feels that U-DO is going to cause the universe to collapse, after he lost his mind during the U.M.N experiments when he made contact with U-DO. Krelian is trying to use the Zohar to ascend humanity to a higher plane of existence to end human suffering, which is why NeoCracker, Elly states Krelian was a kind person, his entire goal was to make it so no one would ever suffer again, it just involved resurrecting a machine god and awakening the true god, so humanity could ride its coattails into a higher dimension. He pretty much states this in-game. :p Though I will say that I feel the Yuriev/Grahf is another valid choice Forsaken Lover.
Both figures are very tragic, and both have their asshole aspects about them. To me, this comes down to whether you want interesting (Yuriev) or empathetic (Krelian) Krelian has the better character development and he's ultimately a less cartoonish villain than Yuriev, but I also can't really count out how utterly original Yuriev's storyline is, whereas Krelian takes cues from Neon Genesis Evangelion, to me it depends on what you are in the mood for.
Winner - Tie
Margulis Vs Karh Ramsus
Why are they paired - I defer to NeoCracker's post. I would also like to point out that Margulis and Ramsus have the same intros into their stories, with both characters arriving at their new base of operations and immediately interrogating a little girl for valuable information for their respected organizations. They also dress in similar clothes.
Ramsus was a man created to be the ultimate key in Solaris' plan, a copy of the aging and decrepit Cain, before he was fully grown he was cast out because Miang had discovered the Contact whom Ramsus was suppose to take the role of. This being shun before he was truly born ultimately gave Ramsus an inferiority complex that drives him and hinders him. Marguilis is a religious zealot who wants to return to Lost Jerusalem because his religious faith states his people will return their one day... which is about all I can say about Margulis. Ramsus to me is just the more interesting character because he's more multifaceted. You see the good and bad in him, and the way the other villains cruelly use his inferiority complex to manupulate him makes him a far more sympathetic being. He simply wants to belong. Margulis is just a unscrupulous zealot whose unaware of being manipulated 9course we get no real details either until the last game) but ultimately... smurf Margulis conviction, I'll take a more tragic and interesting figure (a side villain no less) over a generic military asshole who believes "the mission is everything". Now don't get me wrong, I like Margulis, he was one of my fave guys, but against Ramsus, I feel its clear that Ramsus is just a far better developed character whereas Margulis gets little to no development throught the series. Ramsus could technically fight Elly on equal footing as the secondary main character since a lot of Gears' story is about exploring him and his past.
Winner: Ramsus
Albedo Vs Grahf
Why they are paired - Both initially appear as rather cartoonish villains who then quickly usurp that assumption by being crazy and insanely powerful, and ultimately both characters emerge as their games most sympathetic and likable characters. They're both softies as well but you won't know until your a ways into the plots. I also feel that pairing either character up with anyone else but each other would have made for a one sided deal. I mean techinically an argument could be made for Yuriev and Id to face off with each guy but I kind of feel that both of these guys are so well rounded, they knockout the rest of the competition.
I could go on about what makes both of these guys great, but I don't have that kind of time, so for me it comes down to weaknesses. For Albedo, I feel his story arc jumps around way too much and while it all still makes since when the smoke clears, his motive throughout the games has been much like his personality, all over the place.They also kind of jump the sympathy card pretty early on him, even in Episode 1 you have enough details about his past to feel bad for the guy, Epsidoe 2 just took it to a whole new level, and by Episode 3, his actions clearly have him in the good guy territory. I honestly feel that Albedo does outstay his welcome, Episode 2 (before the final scene) would have been a great conclusion to his story but he's a fan favorite and gets brought back for the third game where he largely doe nothing until the big showdown with Yuriev, so I kind of feel Albedo's story is weakened in the end because his time as a Testament seemed kind of wasted potential to me, it isn't helped that his charming qualities of being battrout crazy is totally absent in this game either. He just ultimately came across very muted, which seemed like a sad way to end such an energetic figure.He still gets a nice ending, but I kind of feel the writer's overextended their hand with him.
Grahf... Is a bit too cartoonishly evil for a long time in the game, while he proves quickly he's a badass, he takes much longer to develop into someone who doesn't look like he stepped out of a Super Sentai series. By the time you reach the end of Disc 1 you're kind of wondering what's going on with him because he's saved Fei and Elly's life a number of times and he comes across more conflicted than the sure MWHHHAHAHAHA evil he started off as. Disc 2 pretty much lays his story on thick for you, but sadly after the revelation of his past and who he is, you only really get one more scene with him so the pacing of his story is off for my taste. He still gets his final moment where he redeems himself but it does feel forced due to the games rushed finale.
Winner - Tie Don't make me choose :cry:
Herman and Richard Vs. The Elements
Why they are paired - They are the recurring flunkies the game tries to convince you are all that, but are largely pushovers.
The Elements got this, largely because they are quirky and fun to watch on screen, whereas Herman and Richard get absolutely no character development and you only find out any info on them and what they even look like (their always piloting their Mecha) unless you go through Japanese only source materials or read the datalogs in-game. The Elements at least have a bit more story and rationale as to why they stick by Ramsus. They are also a Super Semntai team. So extra points their.
Winner - The Elements
To me there are no other real comparisons. The Gazel Ministry, Id, The Testaments, and even Elly's Lamb Unit have no really comparable counterpart. I'll do my write up the heroes when I have more time.