I really enjoyed VS System. The game was really well designed, and initially captured the feel of what you would expect from a comic book beatdown. I think my favorite decks were an Emperor Joker mill deck and a Neutron deck. I never bothered to take those to competitions (I generally was a lot more 'traditional' in my deck choices when I was playing at those, but some of the card interactions that I was playing with online via OCTGN were pretty funny and enjoyable to run. Especially when you go up against someone who has no idea of what is about to happen.
My favorite 'competitive deck' had to be Teen Titans though. I know a lot of people didn't like the Roy Harper/TTG/Press the Attack abuse, but when I first built a Teen Titans deck and really got around to playing it, I realized it scratched all the itches of a combo deck that I wanted in the game.
Damn, I can tell you've been around.
My stint with VS started the day my local shop got their first shipment of Marvel Origins. I wasn't really tuned in to the internet so I didn't know anything about it - mainly just frequented Pojo for Yugioh stuff. When I came in, it was a slow day, and one of the employees I was pretty friendly with said "hey, sit down over here, I want to show you something...". Needless to say, the game blew me away. Formations alone boggled my teenage mind, I just never saw anything like that in a card game before. Rest was history, at least until around JLA when the game died out locally. Though I was fortunate to take top 8 in a local PTQ with Curve Sentinels and basically no practice lol (though I lost to Marvel Knights, which I had never seen before). Besides that, Common Enemy was always a favorite. Turn 7 Mr. Fantastic + Kevlar Body Armor into Turn 8 Silver Surfer was always a crushing play, and I loved having Mystical Paralysis on turns where they had the initiative. Also loved the "fuck it, all in" nature of Squadron Supreme.
I know a guy who used to be the authority on Teen Titans. It can be a frustrating deck to play against, if only because it seemingly bases its strategy on exploiting a loophole in the rules - that an attacking character will ready if the defender becomes stunned, even if the character readied and exhausted for an activation cost during the attack. The Roy Harper stuff was nuts for that reason, but it's whatever. I tech'd Micro Sentinels against them, but it was still rough. Titans just has such amazing support cards in addition to Roy and TTG. Optitron is basically Pantha and a free search if you drop it turn one, and Argus is nasty with Terra (who is also nasty). Turn 2 Pantha, Turn 3 Hank+Dawn, Turn 4 Terra, Turn 5 Roy+Win (basically) is a crushing series of plays. Even if it doesn't work, you have motherfucking Garth who enables all sorts of shenanigans with stuff like TTG and Titans Tower + Starfire.
Man, it's all coming back. I really hope they knock it out of the park with the reboot.
edit
We have a Batman starter set (or two?) that I have yet to really figure out how to play.
It's absolutely a difficult game to learn. If you have any questions, feel free to post them and I'm sure either I or RyanDG can answer them.