I read somewhere that to find out the actual power of a move, you multiply the accuracy with its base power. Since Thunder has a 70% chance of connecting, it has an average base power damage of 84, which is 11 points less than Thunderbolt.
So, unless you have a Rain Team or some funky setup to allow Thunder to hit 100% of the time, I'd recommend going with Thunderbolt instead.
Random GameFAQs user in regards to a used game: "No tutorial since its from GameStop."
Thunder may be able to OHKO something that Thunderbolt can't.
So it's all about power vs. accuracy. The average damage would tell you that you should use Thunderbolt to be accurate, but there will still be people who want to take risks for the potential of more damage.
In some cases, the extra damage can be the difference between a KO or not.
I know some people who go with the more accurate choice in single elimination, and risk things more if it's a best out of thing. If you've got to win 2 of 3, you have more of a buffer for misses and the RNG not going your way.