Okay, this has annoyed me for the better part of a year. The campaign events are pushed with a narrative (often poorly written) indicating a specific theme. Now, given that the Common, Uncommon and Rare cards haven't been expanded since launch (albeit with a few Episode Rares) the pool of cards from which to select enemy waves is rather shallow. Mobage has thrown a curve ball every now and then, such as using Super Rare cards for bosses, but otherwise the Enemy Waves haven't changed much, if at all.
Originally we could count on distinct Autobot and Decepticon waves, depending upon the event theme (as determined by the weapon bonus, IMHO). As I stated elsewhere,  that has apparently been abandoned by Mobage recently. Perhaps its due to staff changeover or layoffs due to Obamacare. Who knows?
That said, the existing Enemy Waves are both perplexing and annoying in their composition, or force structure, if you will. You have nearly thirty years of cartoons, comics and toylines from which to glean contextual storylines that would suggest members for these Enemy Waves. Conforming to that data would thrill the players far more than the apparently random composition to this point, and eliminate the head-scratchingly painful assortment of "dual members", or waves in which there are two of the same card (I'm looking at you, Silverstreak).
For example, there are Autobot waves that consist of Blurr (A) & Sunstreaker (A) being "led" by...Swoop (A)? Or Slug (A) leading Sideswipe (A) & Sludge (A)? Or Cliffjumper (A) leading...Cliffjumper (A) and Slug (A)? Sludge (R) leading Blurr (R) and Cliffjumper (R)? It doesn't make sense! Especially when there SO many other combinations that make sense and are viable given the range of available cards.
First off, make sure that the proper faction is being paired. Then, simply create 3-man teams from existing known teams. Such as:
Dinobots: Slug, Sludge, Snarl and Swoop give you a plethora of combinations, with Grimlock (Rare) as a boss or added to up the Deck Power in Medium or Hard campaigns.
Minibots: Gears, Huffer, Windcharger, Cliffjumper, Warpath, Bumblebee, Brawn...all are interchangeable for "team" purposes and would fit in nicely as characters in the "Easy" campaign.
Autobot Cassettes: Eject, Ramhorn, Rewind, Steeljaw, all paired with Blaster in various combinations. You're welcome.
Autobot Cars: Prowl leading Silverstreak and Smokescreen would be awesome. Trailbreaker(-cutter), Ironhide and Hound would be sweet. Inferno, Red Alert and Ratchet would team nicely, from a theme standpoint. Sideswipe, Sunstreaker and Tracks would make sense, maybe swap Tracks for Red Alert for an "All Lambo" team. Wheeljack, Ratchet & Hoist would work. Mirage, Jazz and Wheeljack would be sweet for the Hard campaign. Grappel, Hoist and Huffer (minibot) would work, too.
Team Cybertron: Blurr, Kup, Perceptor and Wreck-Gar teamed up with Ultra Magnus. Easy enough. Throw in a Chromia for fun.
Cassettes: Too easy. Rumble, Frenzy, Buzzsaw, Laserbeak, Overkill, Slugfest, Ratbat, Ravage all with the option of being paired with Soundwave in various combinations. I guess you'd have to include Reflector here, since he doesn't fit anywhere else.
Insecticons: Hardshell, Kickback, Sharpshot are obvious, as is Venom, Ransack, and Chop Shop. Mix as needed.
Predacons: Razorclaw, Divebomb, Rampage, Headstrong. No Tantrum, though.
Combaticons: Blast Off, Onslaught, Brawl, and Vortex. No Swindle, oddly, as I mentioned back in October [].
Consructicons: Mixmaster, Scavenger, Long Haul, Hook, Bonecrusher. Yet they're shy 1x constructicon.
Seekers: Again, too easy. Team up Dirge, Thrust and Ramjet, then have Starscream, Skywarp and Thundercracker. Acid Strom and Slipstream are the wild-cards. I'm surprised this hasn't happened yet, even in episodes that feature the seekers.
In short, teaming the Enemy Waves in the manner I've described makes FAR more sense than the seemingly random method that's currently in place.
Team Cybertron: Scourge, Cyclonus and Galvatron, obviously. Maybe Shockwave?