I have always believed that having the right combination of offense and defense can be a major recruiting advantage and practice plan advantage, especially if you don't have an A Prestige. When you combine an offense and defense that require the same skill set, it allows you to focus on recruits with a handful of skill and target more practice minutes on those skills for faster development. If the combination of offense and defense does not match up as well, you may have to decide if you are recruiting an offensive player or defensive player, or if the recruit needs to have high potential in a lot more skills. Then you have to decide how you are going to alocate your practice minutes on all those skills. 

High WE also becomes a major priority if you have more skills to develop. Add to that the fact that certain offenses and defenses require a higher level of IQ.  It is an advantage to have either an offense or defense that does not require an A IQ to become affective.  That way you can focus a few more minutes of the one that does require an A IQ without sacrificing practice minutes on the skills. This is more critical when you have a young team.
 

That all being said, most of the offenses and defenses match up pretty well. There are only a couple of combinations that require different skill sets. And the better the Prestige you have, the less it matters due to the quality of the recruits you see and the balance in their skills and potential. There are a couple of great threads for new coaches and you can read what skills are needed for which offense and defense. You can also look at some of the basic combinations that the top coaches use. Some have already been mentioned here. 
 

Many years ago I re-read all the threads, 101, etc., and put all the skill levels required for each offense and defense down on paper. I then looked at the combinations used by some of the best coaches and the level of skills they had with those offenses and defenses.  I then created a list of all possible combinations, from most compatible to least compatible. I don't have it any more but it was easy to do. I don't know it was anything earth shattering, but I found value in doing it early in my HD years and it helped me to better understand the game.