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Skills are going to be handled just a tiny bit differently, with a homerule texture. 

There is a world of difference, in my mind, between someone trained in a skill, and someone who is not trained in a skill. What's the difference? Knowing how to use a skill to it's best advantage. I'll use diplomacy as an example.

Someone who has been trained in diplomacy has been schooled in regional traditions, dialects, cultural differences,   and the best use of body language and wording. 

Someone who has not been trained in diplomacy is a generally likable person who has a knack for getting people to like him and want to cooperate with him. Someone trained in diplomacy generally has that working to his advantage as well.

Because of these differences if you were untrained in diplomacy you could only use it in select situations. For instance, you're travelling in the region you came from. This would mean you don't need specialized training in diplomacy to know the regional traditions, dialects, culture, etc. You wouldn't receive a bonus for being from the area, but if you wanted to influence someone to do something they might not normally do, you'd be able to make the attempt without having your lack of training play against you (in other words, without having your DC increased).

On the other hand you're in an area where the culture and the people are very different from your own, untrained there would be a much higher DC for something of that nature. However, asking the local tavern owner, who happens to be a rather surly, antisocial, grumpy, kind of fellow for directions, the DC would be the same trained and untrained. 

Most skills will be the same, trained or untrained. Athletics, Acrobatics, Perception.... things like that don't change. Bluff? It might depend on your situation and what you're trying to accomplish. If you're trying to convince the constable that you're not actually breaking the law, when you are, he's going to be different between someone trained and untrained. Trying to convince the woman milking the cows that you're not breaking the law is going to be the same, trained or untrained. 

Arcana and Religion, these are tough ones. I'll use some mysterious magical barrier as an example here.

Someone untrained in arcana rolls a 24 to see if he has heard of something like this before.

You know that this is a fairly powerful magical spell. You suspect that you and your party would have very little chance of disabling this yourselves. You're fairly certain it's drawing power from somewhere else.

Someone trained in Arcana rolls a 24 to see what they know about the same magical barrier.

You know that this is a fairly powerful magical spell. You are quite certain that, aside from destroying the barrier's power source you have no chance of disabling it. You can sense the power currently being maintained by another magic user, far beneath you. You can feel both death magic and life magic flowing through the barrier.

Why the differences? Well, the first guy has heard a LOT about magic. He's heard of this type of barrier before, so he has some ideas as to how this one works. His knowledge of magic spells is on par with someone who is actually trained in the use of magic. However, the guy trained in Arcana is actually trained in the use of magic. He can feel the magic, interpret things from it, feel how it moves and so forth. It's the difference between general knowledge and applied knowledge. 

In short, just because Bob and Harry have the same result roll, doesn't mean they have the same result. I could go ahead and do negatives for each roll, but it's easier for me to simply maintain multiple DCs for different things. I know this isn't WOTC approved, but for me it simply makes sense. If there are questions, comments, complaints, let me know, I'm open to hearing them.

(Note, in all but the weirdest of cases your physical skills will be the same. Unless you give me a reason why your trained skill should give you an easier DC than someone else)