If you run the alt straight to the battery, you will no longer be able to run the engine without a battery.
Stock, you can start the engine, then remove the battery and it will still run, because the alt is supplying all the engines demands.
Also, the volt reg senses the voltage & current needed for the vehicle, NOT the battery. It supplies this and charges the battery at the same time. That way, the battery will charge up AND the vehicle will run.
If you send all this straight to the battery, then as soon as you turn the vehicle off, the battery will be low, since the alt will only be supplying what is needed to recharge the battery. Stock it supplies the vehicle AND recharges the battery. If it goes straight to the battery, it will only charge the battery, while the battery is being sucked down at the same time by the vehicle.
The alt cannot instantly do a full recharge on the battery. So, if you run the alt to the batt, after you start and stop the engine a few times with a short recharge period, you will slowly kill the battery. You lose the full electric power to the vehicle with the excess recharging the battery. Now, you only charge the batt, and you are doing so at the same time it is being drained.
It's kinda like running my laptop off AC while the battery is being charged. If the AC only charged the battery (same as running the alt straight to the batt), I wouldn't be able to use it (like I am now) while the battery is being recharged, until the battery has been recharged enough to run the computer.
Also the battery is kinda a backup power supply for the vehicle. Stock, the alt supplies the vehicle, and when the alt dies, the battery does this until it dies. You don't even need a battery if you jump start it.
If you run the alt to the batt, it will work the same way, but the battery won't be at full charge when it takes over, and it won't nearly as long, since as the alt is dying, the battery charge is dropping. You lose the redundant safety factor of 2 power sources running the alt to the batt straight.
If the gage of wire is what concerns you, upgrade it, but don't run the alt to the batt only.