It depends on what's more important to you. If it's a bigger house for your $ then Temecula is a better option. Temecula also tends to have better schools for the kiddos.
The drive to Oceanside/Pendleton sucks. What you are saving on the bigger house goes right into you gas tank and vehicle maintenance especially when you add in all the additional wear and tear on your vehicle and how much more frequently you need to service the vehicle due to all the miles being put on it. (oil changes, new tires...etc).
It's also usually about 10 degrees hotter in Temecula then Oceanside at all times due to it being more inland. So if you aren't a fan of the heat expect a higher electric bill running that AC.
As mentioned the fallbrook gate is a mess most of the time. When i lived in Murietta i actually took the 15 to the 78 and entered Pendleton from the front gate most days. It was more miles each way to and from my house, but less traffic and i actually made better time despite the increased distance.
Personally i think the whole Temecula/Murietta/Menefee area is over-rated these days. It was the place to be in the mid 90's when it was still being developed and new, but now it's over-crowded and the value of the homes has leveled out and they aren't as much of a deal as they use to be.
I live in Murrieta and I love it! Great people always some thing to do... also your away from constantly being around Marines... I Highly recommend it. My husband works on the opposite side of the base in SOI.... it gets hot in the summer but we have air condition. I lived in San Clemente before we moved out here and if i had to pic between the two I would def pick Murrieta!