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Abuse
It's unfortunate that some guys will abuse the situation by blatently using players out of position, but I say so what.  The game can create enough penalty to hurt them in the long run. 
It's when a manager gets severely penalized because of circumstance that I don't like.  I had my centerfielder get a daily injury, and his replacement gives up 5 errors.
Somebody mentioned that defensive ratings should be a combination of the last two seasons.  I like that idea.  For example I have Tony Batista.  He was an ODR 6+ rated shortstop, but switched positions so all of a sudden he's useless at short?  I got Pat Meares, a guy who had played short his entire life, and now hasn't played there this year.  It seems like I'm constantly looking for a shortstop, even though I have two players that are quite capable of playing the position.  If there was a two year rating then it gives you more time to trade or draft to improve the weak position.
I know the first response is why not make a trade immediately.  Too often when guys see that you're weak at a key position they expect to get a bargain because of it.  I get nothing but stupid offers because they think I'm "desperate" for a key position.  To hell with that.  I'll use an innoc player before I'll accept a rip-off offer.  I don't want to severly weaken my team simply because the game has defensive inflexibility.
I guess it's a fine balance.  Create enough penalty so that abuse is avoided, but don't severly penalize a legit manager because of circumstance.  Sometimes a little defensive flexibility is required, and nobody should be forced into making a deal they don't want to do.