There is no sensible discussion to be had while this topic is examined on such broad terms. The lower accuracy of Thunder is a great disadvantage, but simultaneously its greater power is a great advantage. The choice between Thunder and Thunderbolt should always be approached in the context of a specific Pokemon, often on a specific team.
Each Pokemon has varying factors in the number and importance of targets for Thunder/Thunderbolt, the tendency of those targets towards a certain weather, its ability to achieve significant OHKOs and 2HKOs on said targets without the additional power of Thunder. Xerneas, for example, often relies on Thunderbolt or Thunder for broad coverage and must use it often, while Palkia mainly uses the move for Kyogre and Water Arceus due to its other moves' excellent coverage. For Geomancy Xerneas, all targets are important, as it seeks to sweep an opponent. For Palkia, Kyogre is a very important target, as one of its primary roles is typically to check Kyogre. For Pokemon such as Mega Mewtwo Y, Thunder is merely a coverage option, and it can switch out quite freely against targets that may survive Thunder or if using Thunder is risky due to unfavourable weather. Targets such as Ho-Oh are more commonly found in Sun teams, reducing the chances of Rain or neutral weather that favours Thunder, while Kyogre is an easy target for Thunder due to its ability. Perhaps most important, however, is the consideration of the power difference. Many offensive Pokemon cannot afford to fail to KO an opposing Pokemon; the choice between Thunder and Thunderbolt can easily be the choice between a 70% chance of winning an encounter one on one and a 100% chance of losing it (albeit having dealt considerable damage). Pokemon with very powerful STAB moves also gain very little coverage through Thunderbolt; a neutral STAB Hydro Pump is only a little weaker than a super effective Thunderbolt, and a resisted STAB Fairy Aura Moonblast is slightly more powerful than a neutral Thunderbolt.
Once all of these factors have been considered, the weather of one's own team becomes worthy of consideration, and can be used to mediate the decision between Thunder and Thunderbolt. Sun of course favours Thunderbolt, while rain favours Thunder, and neutral weather cannot be thought to favour either. However, all in all, no declarations can be made of the superiority of either move, as it varies greatly across the moves' users and teams.