Both Peter Parker and Miles Morales will continue to have their separate comics after the Secret Wars (this supposedly big event/reboot that is happening).
Miles Morales is this guy and Spider-Gwen is this woman. Also, she has the best costume Marvel has designed in many years.
They have slightly different abilities and very different personalities, but in the end, in a game like this they would probably play very much the same.
The Hulkbuster is just a new Ironman armour, namely the MK 44, and that actually is an add-on and goes on top of another armour. For reference, the armour used in Ironman 3 is the 42, in the Ultron movie both 43 and 45 are used and I believe that the Disney Infinity figure is based on the MK 7.
The new female Thor is not the case that Thor became a female but that another character picked up the hammer and got almost the same powers as Thor Odinson.