Probably the biggest difference is the ability of the incandescent flash to capture color pictures even during the nighttime. If the flash is used in the daytime it will not have any effect on the picture as the amount of daylight is so strong that it just washes out the incandescent flash. The actual picture quality is better with an incandescent flash and higher resolution is achievable. These are the advantages. The drawbacks include the fact that it simply takes more energy than an infrared flash. This really causes two issues, first, the batteries on the camera will deplete faster. Second, the batteries need to create a surge to supply enough power to use the incandescent flash. Sometimes time is a factor when you want to get a shot and you will definitely see hesitation in the trigger of the incandescent flash. It is a powerful flash, and as such it will tend to scare off game pretty much every time. Nobody will mistake where you are when you use it, whether it is game or other people.
The Infrared Flash
While the picture quality is not as good as the incandescent, that is about the only drawback to the infrared flash when you are considering it as a flash for a trail camera. The infrared flash will not scare off the game that you are capturing, and it will not give away your position to other hunters or curious folks either. Because the infrared flash takes significantly less power to use, your battery life will be enhanced and you will also be able to power up much faster than with a conventional flash. In the daytime, you can have either color or black and white photos, but in the darkness only the black and white is possible. The pictures will tend to have a little blurriness as compared to the incandescent flash shots.
Which one is for You?
Not all animals are the same, and some of them just aren't spooked by the incandescent flash. The problem is that most of them are. You have to look at what you are using the camera for. If you are taking shots for a magazine, then you are looking for the best picture quality and this would be from the incandescent flash. Most of us are not, and in most cases it will matter whether or not you are scaring off the subjects of your shots. For stealth, the infrared is the way to go. In terms of convenience the infrared wins out as well because of the longer battery life and faster trigger speed. Another factor is that you will get more shots with the infrared as you aren't scaring away your subjects. It makes that extra battery life all the more necessary.