Its one thing to appear as 'agent' for someone, and something totally different to 'represent' them. In Ontario, you need to be a lawyer or paralegal to represent someone in traffic court. Section 82 of the POA allows a person in traffic court to act by representative. The definition of "representative" in section 1 says that is "a person authorized under the Law Society Act to represent a person in that proceeding". Under the Law Society Act, that means you are either a licensed lawyer or paralegal.
It would be very unfair (especially to paralegals) to allow lay-people to represent others, including family members, since that would create a loop-hole in the system of professional regulation. After all, paralegals (like lawyers) must now also abide by professional rules, pay dues and pay insurance premiums. If others were allowed to represent someone without being subject to the same professional limitations, the regulatory system would be unfair, not to mention, potentially put the public at risk for having unqualified individuals 'representing' others. It would defeat the purpose of the professional system of regulation.
Just know though that often times, courts WILL allow non-licensees to appear as an 'agent' for someone. That is, they are merely attending in place of the accused to enter a guilty plea or seek an adjournment----they must follow the instructions of the accused and are simply there to vocalize the accused's wishes. However, the moment that person attempts to make a motion, proceed to trial, or do anything beyond preliminary matters, the accused must either attend and self-represent or retain a lawyer or paralegal. After all, at that stage, 'legal services' are now required, including potentially interpreting laws or procedures, giving legal opinions, making submissions to the court and/or forming trial strategies. That's quite different from just being a messenger!
In your situation, your wife wasn't present and she likely was the accused. If you had instructions from her, then you should have been able to enter a guilty plea on her behalf and then make submissions regarding the fine. However, serving as an 'agent' is not an automatic right----the court has discretion on whether to permit you to appear as her 'agent'. Why your son got involved in this case at all is beyond me---after all, he was merely the driver. Red Light Camera tickets go towards the registered owner of the vehicle, so any submissions about your son's financial situation is irrelevant----he's not the one who is legally liable for it; your wife is.
I don't know if your son entered a 'not guilty' plea on behalf of your wife, or whether he entered 'guilty' and then spoke to the fine. Regardless, your son's financial situation is irrelevant---he's not the accused. So, if he started talking about HIS financial situation, the court would likely not adjust the fine in anyway----after all, the court would not have heard any evidence with respect to the the accused; instead it heard submissions about your son's finances. Furthermore, if your son was doing the talking, then more than likely the court allowed him to be your wife's agent. Why would a person need more than 1 agent? Perhaps that's why they didn't allow you to speak on her behalf.
Bottom line: you guys should have done your homework on these issues before proceeding to court----you definitely should have coordinated things better and determined who was going to speak on your wife's behalf. This only shows that your son wasn't the only 'rookie' on the team that day---reaffirming the need for professional regulations of legal representatives! 
Finally, I'm actually surprised that the prosecutor didn't just offer you a reduced fine; that's usually how those offences are resolved. Hopefully you guys weren't just being greedy and thought you'd get an even bigger reduction in court----that almost never happens!