Picked up the enhanced edition and have been playing two player games. We have lost all seven games we have played so far. This game seems tough! Our first game was Omnitron against Haka and Absolute Zero.
I would suggest playing at least 2 Heroes each. As the game is designed with 3-5 Heros but can be played 2-5. Its not widely advertised but Page 11 does say if you are playing with 2 players its advised to play with 2 each.
Though even then the game is tough 
This game is not balanced if you play only with two heroes. It is not intended to be. Most villains does not work if H = 2, and other are almost imposible to beat. If you want to play the game only with two players, either both of you must control 2 heroes, or one of you have to control 2 heroes and the other only one.
This fact is clearly stated in the online tutorial in the SotM (Sentinels of the Multiverse) web page, and it is stated upfront. But, in the Enhanced Edition, it was not clearly stated.
If you want to check, in the second page of this tutorial:
http://sentinelsofthemultiverse.com/gameplay
Note: each game will have three to five heroes, so with just two players, one or both of the players can run two heros. Don't worry! Hero turns are easy.
Another omision in the Enhanced Edition is this:
Whenever you need to draw a card from a deck, or play the top card from a deck, and that deck is empty, you have to shuffle the trash corresponding to that deck, and form a new deck. (Note: heroes maz draw a card in their drawing phase each turn, but they don¨t have to)
So, good luck with this new perspective, and welcome to the forums!
When I started writtin my response there was none, but I am too slow writing in English... Also I wanted to provide sources and such.
But: my understanding is that it is compulsory to play at least with 3 heores, not "advisable". The fact that it is not clearly stated in the Enhanced Edition Rulebook is an error of the rulebook.
(Of course, you can play only with two heroes if you really want, as an atypical SotM experience. You can also play against Citizen Dawn but substitute all the "Devastating Aurora" card with cheese slices. It´s your game, it's your house. :P)
Well, thanks for the information. Would have thought the enhanced edition would have had a better rulebook.
I believe it was supposed to, but an earlier version was accidentally the one that was printed and included.
I think the enhanced edition was a big improvement over the first one. Better mechanics, art in the environment cards, better box which is a suitable storage solution, full art separators, life counters, effects markers...
The rulebook has some errors. But after the first games you don´t play with the rulebook.
(But I understand your frustation after 7 games... )
Why did the rulebook not get fixed in the second printing then?