After playtesting Ambuscade a bunch, we started playing that he starts with all of his traps face up. It made him more challenging.
I like that idea. Seemed weird to me that you could draw a trap, shuffle it back into the deck face-up, and if it ends up close to the bottom, never see it again during the fight.
It will certainly make him more challenging and entertaining to play against! 
Or maybe you could play that if you draw a trap, rather than shuffling it randomly back into the deck, you could always place it face-up a certain number of spaces down in the deck, i.e. a trap will always go off three (for example) draws after it's first encountered.
This is an interesting topic. It's basically different for all of the villain/hero pairs, but I think for the most part that each of them do a fine job of playing off each other. Sometimes you have to look at things differently in order to appreciate it, but it's there for all of them.
For some of them, the link is more thematic in nature. I don't know how you could fight Voss and NOT want to play Tempest, from a thematic standpoint. To be there spouting off angry dialogue about vengeance for destroying your planet is probably a good part of why we play this game.
Expatriette has the mechanical link others have described, but she also has great thematic links that I don't think I've seen pointed out here. Citizen Dawn has all sorts of Communist imagery, not least of all the card back and the freaking name. Expatriette is clearly a Republican member of the NRA.
Matriarch/Tachyon feels like more of the mechanical link, and I find that works just fine for me.
There's other fun dichotomies. I'm sure I'm not the only one to notice that Haka, the hero with the most hit points, is opposed by Ambuscade, the villain with the least. Inversely, Argent Adept has the fewest hit points among heroes, and Akash'Bhuta has the most among the villains, at 100% more than the closest contenders.
One more, and I'll shut up. The relationship between Apostate and Fanatic is perfect. Aside from the ironclad thematic link, there are a bunch of cards that are mirror images of each other, and they're both extremely good against the other. Fanatic can tear into Apostate like no other, but she can't win the game on her own. This is how it's done.
One thing between Haka and Ambuscade, if Haka keeps taking his devices with Savage Mana, he'll have more chances to combo where he shuffles the trash and plays the top card and will make the traps come up more often. I remember shuffling his deck like 5 times or so in a single turn once, and that was without Haka stealing his toys. And I believe one card reveals until a device is revealed, if less devices are in there, the better chance a trap that's been armed becomes the top card.
That's true. When we played Ambuscade a few days ago at Gen Con, he got a ton of combos, but that was without absorbing his gadgets. He got "Run 'n' Gun", we reshuffled, and he got it again. And this happened in two different turns. Then he got a "Run 'n' Gun" and "Quick Stim-Patch" combo, so he was pretty much playing three cards every turn.
Good lord. Ambuscade "Run 'n' Gun'd" every turn we played. I could've killed his fictional being.
Yeah, but I guess it makes sense that Ambuscade can do that, since he's got the lowest health of any villain (not counting individual members of The Ennead). He's easy to kill, but he's got an equal chance of winning since he hits pretty hard. He's like the sabre cats in Skyrim. Don't worry, Dakota; you'll understand what I mean once I let you have our copy of the game.
Awh, man! I just spit Dr. Pepper all over my keyboard.
So what would Unity's nemisis' deck do? Destroy hero cards to bring out minoins?
Perhaps an old school mate that instead of technomancy used biomancy for similar effect. Plus she ended up on the freedom five despite not being able to pay enough attention in college, but he worked hard and graduated top of his class and still didnt get in. Thus he turns into her bitter rival and a super villain to boot.
Yeah, I've got a feeling Unity's nemesis will be very biological-based. I really can't wait to see her nemesis. Since she's my favorite character, I want to see her really fighting hardcore against someone.