If I only have one dime defense in my playbook or one goalline defense, do I actually get penalized for overuse? Or do I just get the annoying overuse message?

You'll just get the message unless you have a rule that puts it into play against normal offensive personnel. Technically your opponent could be doing better because they are gaining familiarity with the play, or because they scouted the play, but there is no additional overuse penalty for any defensive play when the offense is in a personnel with 0, 3, 4, or 5 WRs.

Why do you even get the message if you're not going to be penalized for it?

Also, are 3 WR sets considered to be some kind of spread offense in this game or something?
Why should you be able to run the same blitz play every down against these sets without the penalty kicking in?

This whole abuse thing is pointless if it is going to be this limited and toothless.

I was wondering about the 3 WR set. That should be a "normal set" that defaults to the Nickle defense. Why should I be able to run the same Dime defense against the 113 or 203 all game when I have 12-15 Nickle defenses?

Also, do I get penalized if I use a rule to call Dime defenses against the 005, 014, and 104 so that I'm always calling Pass Key?

And, for WarEagle, I don't always call the Dime Blitz 2, but when I call the Dime, I call the Blitz 2.

Initially it applied to all plays, but because of the ability for offenses to force a defense into playing all nickel or dime I felt that it was giving an unfair advantage to someone who could use that to game the system. So the play-by-play is actually tracking the number of times a play is used and if it's overused and a negative play results, it shows that. It's not completely incorrect because your team does improve against the same play the more it sees it, even without the penalty. The penalty is just there to combat what really is a bigger problem - and ultimately I want to have the engine more properly address the problem and do away with the artificial penalty.

What essentially happens is that the penalty logic is skipped if the offense comes out in 3+ WRs or 0 WRs, so yes, your dime will get a familiarity penalty if you deploy it against 1 or 2 WR sets.

So in essence, there is no penalty to discourage someone from calling just a handful of defensive plays (or even just 1) against your Offense, unless you want to line up in pop warner formations all game.