There is no real way to play Marvel, it's a very creative fighting game compared to most given the variety of tools on offer. This is generally what scares most people off playing since it doesn't 'make sense' to other fighting game players who are not used to having such a wide range of options available (add to that the fact that many traditional fighting game fundamentals do not matter as much or are far less effective, such as the classic fireball/uppercut game).
In all honesty though (trying to be unbiased here), marvel 3 is probably the easiest fighting game to pick up and be competitive at in a short amount of time. Plenty of easy mode chars with dial a combos and xfactor do a lot to mitigate the skill difference between advanced and beginner players, and all the different options you have generally start to make sense within a few months of solid play. Saying that, the game is also very gimmicky, and given it's fast pace some things will drive you nuts trying to block in the initial stages.
The first thing you should ask yourself is what sort of team do you want to play. That will answer your question of how you should play the game. The basic categories and Keepaway/Zoning and Rushdown. A lot of chars can be played in both ways, but will excel in one.
Once you've chosen the style you want to play, choose the chars that suit that style. Quick examples for keepaway are Morrigan, Modok, V Joe, Hawkeye, Taskmaster (Note that some of these chars can rush as well). Quick examples or rushdown are Wolv, Felicia, Skrull, X-23, Spencer and to an extent Vergil. In the middle you have chars like Doom, Zero, Magneto and Dorm who can pick and choose whether they want to rush or zone.
After char selection, you've got team synergy to think about. Assists won't take long to get used to, but they can make or break your team. Rushdown chars you'll want a lockdown assist such as Akuma tatsu, Frank trolley, Sent Drones, Doom plasma or missiles. These assists can also work well for keepaway though since they act as a 'get off me' button, or they add to the zoning frenzy (i.e Morri/Doom). Popular team ups are;
Wolv/Akuma
Morrigan/Doom
Mags/Doom Missiles
Zero/Dante
Wesker/Magneto
Vergil/Hawkeye
Vergil/Magneto
The other thing to consider for assist is combo extension. If an assist has no other strong factors about them, it's generally possible to find a combo extender in some form or another if you're creative enough with it.
The last thing to consider is the anchor position. Given that X-Factor gets stronger the fewer chars you have, the final spot can give you access to some pretty scary comeback potential. Team orders generally go Point/Point/Assist or Point/Assist/Anchor, although with good synergy you can find chars that are good anchors and good assists (Magneto is a good example for this). Some of the better anchors are Phoenix (note: A phoenix team will dramatically change the way you have to play your team), Vergil, Magneto and Wesker.
Once you have your team/s that you are thinking about playing sorted, post back up and I'll try to put you on a solid path of where to go.