Long story short: Crisis games are NOT balanced for all of Teen Titan's Ongoing cards.
Deck: All cards EXCEPT Ganthet and Mogo. In retrospect, I probably should have removed some other cards as well.
Super Hero: Picked Crisis Starfire, as anyone besides her and Crisis Hawkman are useless in a single player game.
Super-Villain Stack: Entirely randomized besides Vandal Savage, all Impossible Mode. Stack Ongoing abilities were used even when not on the Super-Villain stack. This was the order:
Black Lantern Superman
Crisis Nekron (H'el)
Crisis Stack: Entirely Randomized besides Immortal Villain, didn't happen to get Heroic Sacrifice. This was the order:
Villains in Disguise
Rise of the Dead
Reshaping Our World
Corrupted Companion (H'el)
Seven Deadly Sins Unleashed
Frozen City (played wrong, forgot to add an extra card at turn start, but wouldn't have mattered)
Draining the Emotional Spectrum
Super-Villains United (Black Adam)
Most Super-Villains and Crisis's were beaten in 1-4 turns, besides Frozen City.
Garfield Logan was in the starting Line-Up, so that helped out a lot. I got Teen Titans Go!, Cybernetic Enhancement, Vic Stone, Daughter of Trigon, Black Lantern Power Ring, two Zoo Keepers, and Cadmus Labs, among other powerful cards and 13 Ongoing cards by the end of the game.
The Colony ended with 14 cards underneath it. I was very quickly able to destroy every Starter in my deck, as well as any Weaknesses I got, and even every Kick I bought.
Multiple times throughout the game I was able to draw my entire deck, thanks to Vic Stone and my many cards that allowed me to draw a card.
The game ended with 64 cards left in the main deck, to give you an idea how easy it was (and how little the Frozen City mess-up would have mattered).
Honestly, does anything else matter?
Crisis mode is NOT balanced for Teen Titans (regardless of player count), and even without Teen Titans Crisis mode is incredibly easy by yourself.
No Crisis expansion targets Ongoing cards, and without competition between multiple players to buy as many Ongoing cards as possible like in a competitive game, you wind up with too many of them and become too powerful.
If you're looking for an engaging experience to play by yourself, just play Crisis mode where you play as both players, not the single player mode.
I find Crisis Black Canary to be least useful when playing with Crisis 2 (and I would assume most useful when playing with Forever Evil to the point of being overpowered, not that I've ever tried it before).
In the Original Set and Heroes Unite, Villains are the only cards that have Attacks (ignoring Yellow Lantern Power Ring and Mind Control Hat), but these are close to useless in a Crisis game. In a cooperative/single player game, that means that any card with an Attack becomes a more expensive version of another card that usually harms your teammates. With 2+ players, you can use these Attacks so your teammates can use Defense cards (and in Forever Evil/Crisis 3 so have stuff like Crisis Bizarro and the VPs to make it so that Attack cards really are worth buying), which won't always work but it's still an intended strategy. But for a single player game, you can't do that at all, since you have no teammates. This turns something like Black Lantern Batman into a Cost 6 card that only gives +2 Power or Black Lantern Martian Manhunter into a Cost 8 card that only give +3 Power.
Because you have to buy every Villain at some point or another, playing as Crisis Black Canary by yourself actually becomes a DISADVANTAGE since you are forced to put these expensive Attack cards with mediocre effects into your deck as opposed to destroying them, as well as any other Villain cards with lackluster effects like Talon. This runs contrary to the nature of Crisis games where since there's no need to compete for VPs you can (most of the time, depending on the Crisis) have each player specialize their decks to be as strong/Defensive/whatever as possible.
Moving on to something somewhat more opinionated, I also think that Crisis Black Canary is still not good in a Crisis game with 2+ players since she is forced to gain every Villain she buys, including ones with Attacks and weak ones she'd prefer not to buy. This forces her to either take losses for the sake of cleaning up the Line-Up or to not clean up the Line-Up for the sake of not taking losses.
Additionally, and I can't believe they did this, Crisis Nekron can not be defeated while a Villain is in play or in the Line-Up. How can Crisis Black Canary defeat him? Now, obviously she can get lucky and get the 15 Power to defeat him, but if you played a single player game and have been forced to buy every single Villain that has shown up, then you're going to have a stupidly difficult luck-based final challenge. I really don't understand why they chose to do this; why create a character who can buy Villains in a Crisis game when the final Super-Villain doesn't allow you to play Villains when you try to defeat him?
I'm somewhat tempted to make a giant list of every Villain that is/isn't worth buying as Crisis Black Canary or that makes her useful, but I could probably turn that into its own forum post.
Teen Titans has a somewhat better selection of Villains available to purchase, but as previously established using the Ongoing Cards isn't balanced well for an Ongoing game. Honestly, I think its probably better to take the Villans WITH Attacks from Teen Titans and add them to a Crisis game WITHOUT playing as Crisis Black Canary, since they're pretty interesting Attacks (and in general interesting Attacks is what makes me recommend always playing with Arkham City permanently in play if you're playing Crisis 1 or 2 with the Original Set or Heroes Unite, or even if you're just playing a competitive game with the Original Set or Heroes Unite along with any of the Crisis and Crossover expansions).
Using Crisis Black Canary in Forever Evil is most useful to her, but to the extent of being overpowered. In a Crisis game (but ESPECIALLY Crisis 3) the cards Owlman, Power Ring, Superwoman, and Ultraman become hands down the most powerful cards in the entire game, but because they're Villains they can't be easily bought. In order to get them, you must first buy/destroy them and then play Black Lantern Power Ring, New York City, or Frankenstein (the latter of which I play Crisis game without), do some fancy Defense shenanigans with both Stargirl and Cosmic Staff, wait for Villains in Control Crisis to (possibly) come up, wait for Permanent Eclipse, Collapsing Parallel Worlds, Alternate Reality, or Villains in Disguise to come up and then get lucky, play Indigo Tribe to buy it (which I would probably remove from a Crisis game with Forever Evil), or do stupid stuff with J'ohn J'onzz playing certain Super-Villains (who I tend to remove from every game besides Crisis with 4+ players). Or, all the way at the end of the game, you can finally buy them from the destroyed pile thanks to Crisis Mazahs! (who basically requires you to buy them as well as restock on Man-Bat Serums if any player still has a lot of VPs).
Or you can just play as Crisis Black Canary and buy them. I don't know about you, but I prefer getting these incredibly powerful cards to provide a challenge to justify you finally being able to play them (right before Atomica shows up and you laugh at yourself as Amanda Waller destroys the card you worked so hard to get so you can defeat the Super-Villain).
And finally, yeah, Time Travel completely breaks a Crisis game. I do wish the games I've played with Legion of Super Heroes saw them sticking around in the Line-Up for a bit longer than they currently do. Most of the time people see them as a tool they and their opponents use until one of them gets enough Power to steal it away from everyone. Maybe I should combine it with a Watchmen co-op game and see how that works...