Great question!
Whenever I play Pokémon, I prefer to begin my adventure with some of my all-time favorite Pokémon with at least two sets of teams, which I often breed from a previous game and transfer to the game I chose to play. Because legendary Pokémon cannot breed, I avoid using them during the early portions of my in-game playthrough because their levels would be too high and they wouldn't listen to my commands anyways until I obtain the required amount of gym badges. However, when I finally do reach the point in the game where I can catch the game's mascot legendary Pokémon or any legendary Pokémon for that matter, I always make some space for it in my party to EV train it, give it a better moveset, and max its friendship. However, after doing that, I box it because I prefer to challenge the gyms and defeat the Elite Four with my Pokémon that I used since the beginning first. After defeating the Elite Four with my primary and secondary teams, I then defeat the Elite Four again with my legendary Pokémon, as I never feel comfortable completely ignoring them in boxes.
Personally, from a storyline perspective, boxing the powerful legendary Pokémon that trainers can most likely catch once in a lifetime and never using it in battle just doesn't feel right, as these Pokémon are simply too rare and powerful to be sitting in a preteen's box doing nothing. This is especially true for Reshiram on a personal level, a Pokémon that I must use whenever I can. On the other hand, when using post-game teams, I have no rules or limits when using legendary Pokémon. During post-game, I literally have hundreds of teams. Some of them consist of all legendary Pokémon while others are comprised of a majority of legendary Pokémon. Some teams might have half their Pokémon be legendary Pokémon, while others might only have one, two, or no legendary Pokémon at all. Some legendary Pokémon are great for certain strategies. For example, Groudon and Kyogre are the best Pokémon to use for Sun and Rain teams respectively.
My point is, if you want to win, you sometimes have to use legendary Pokémon if doing so is the best option. A common belief among various casual Pokémon players is that legendary Pokémon are too powerful and/or "broken," resulting in several casual players refusing to include legendary Pokémon in their teams. However, many casual Pokémon players fail to understand that, despite the video game storylines, anime episodes, and Pokémon movies portraying legendary Pokémon as unstoppable forces, sometimes even with godlike powers, legendary Pokémon are, nonetheless, still regular Pokémon but with a glorified title. Albeit legendary Pokémon are often stronger than non-legendary Pokémon and can definitely make winning battles easier, they can still be defeated in battle with a well-executed strategy. In addition, non-legendary Pokémon can become temporarily stronger than even major legendary Pokémon after using status moves that boost their stats such as Swords Dance, Nasty Plot, Quiver Dance, and so forth.