What Der_Doodle said.
PBeM is long, but if you had to send the file back for every player to determine if they wanted or didn't want to use a skill they have on their player then it would be an extremely long game.
To shorten the game, you hide the ball normally before the opponent sets up for the kick off. Its not required, you could ask for the game back to set the ball up, but normally you don't unless you have kick and it is crucial for you to use it against your opponent. In turn the Opponent normally sets up in a very cover the whole field kinda set up.
Wrestle is another one. People a lot of times assumes you would use your wrestle, so you have to specify that you will not use the wrestle if it causes an early turnover.
Not using dodge when a frenzy player gets the Pushback and Stumble result. If you use dodge your standing on the side line, if you are not using it, he can't push you in the crowd.
Shadowing, can get you in trouble if you are playing against Ogres, the snots just lead your Shadowing player all the way into a waiting Ogre. Unless your opponent says differently, or to lead the opponent off your ball carrier by running a good dodger by the Shadowing player.
And as far as Side Step, the tool has an automatic feature on it for Side Step. So if the player has it, and block them, the tool tells you to use the side step, well its good about it, but not perfect. I have heard of several games basicly lost due to the tool removing the "road Block" out of the way with the use of side step.
There a lot of things lacking in the PBeM compared to the Tabletop.
Common sense would normally tell you not to use a skill, but maybe your opponent would not think of what you are considering common sense, like the dodge example. So its normally just considered unless prior warned, use the skill.
But if its the only way you can play, its better than nothing.

If at first one doesn't succeed, and doesn't try again, then he will never succeed.