I have been playing this awhile, and I've started to view the offense vs. defense situation as kind of a rock/paper/scissors situation. I run a variety of different defenses, and each one of them can stone cold shut down a play. However, if a different play is called by the offense, it will almost certainly be a TD. So, I run a defense to stop that play, but then the first hole is exposed once again.
Obviously running plays with some delay to them is quite deadly if you have the time to let the play develop. Since the defense does not run into the backfield after RB's until they have the ball (they hone in on the QB...or whoever has the ball), RB's can hang around unharrassed by just getting as far away from the QB as possible and not advancing past the line of scrimmage. You can offset this RB advantage by running plays for your TE and WR to get the ball in the backfield depending on the opposing defense configuration.
No matter how you slice it, there is always going to be that rock/paper/scissors element to your play calling in both directions. While one play will score a TD against defense A, it could be a total loser against defense B. This then comes back to scouting and being familiar with your opponent and understanding their tactics and all that good stuff.
Finally, as for skill rating, it is semi unimportant in the greater scheme of things. Defensive players have about 9 categories you need to max. Whatever their ratings are in the other stats (such as kick power, passing, etc.) are factored into your total team rating. Whether they are maxed or barely above 0 in these categories greatly impacts your team rating...but it doesn't change the quality of your players you have on the field. Once again, if this is really a big concern, feel free to scout out your opposition. The best way to compare teams to see how you stack up is to compare your championship levels. Never underestimate the power of that +5 ceiling between each level.