It's not just free exploring that can be rough. Some storyline missons may be very tough, especially if you're flying a cargo ship. On some missions with larger battles, I just flew away a bit and waited for things to clear up. If I charged into combat I had to use bots and sheilds almost continously since for some reason almost all enemy fire was targeted at me (ignoring my allies). A few times I noticed my wingmen flying totally crappy ships, yet they were barely damaged while I was fighting for my life, having to reload saves because I had used too many bots/shields at a previous stage.
Yeah ive gotten better at this game and the free exploring isnt so big a problem for me anymore, but I still have one big problem with this game, which Lim mentioned above. Its that in the campaign (which i beat, but it wasnt so much fun as it could have been because of this reason) every single enemy ship concentrated all of their fire on you. They never, ever shoot at your allies, which i think is totally unrealistic and even more frustrating. sometimes i had to just turn my cruise engines on and fly around in circles like a dumbass and let my wingmen shoot away at the enemy (whom were still only shooting at me)
"Man I am so high right now... i have no idea whats goin' on..." - Towely