Like so many have said, I'm definitely not planning on using my Master Ball for Lugia nor Ho-Oh. This was the biggest mistake I ever made, because it wasn't long when I actually ran into one of the legendary beasts, Entei. So, I'm going to not waste my Master Ball, but keep it for when truly needed.
A few other things I'm going to do differently than before is really train a team, and entire team of six and not only my starter like I did before. Also, I'm going to actually gain an entire team too. As for more onto this, I'm planning on having more of a variety of moves as well as not only sticking to the same type moves for my individual Pokémon. I found this a large mistake later on when I needed coverage against other Pokémon.
Other than this, I'm trying to focus myself into only playing one save file and not messing up in which I'll need to start over. I'm also going to be saving before I confront any major events such as catching Sudowoodo, Lugia, or even Ho-Oh. This is so I can assure I don't have to journey all over their area again to try and capture them if I accidentedly faint them the first few tries. Besides this, I will also change my team up, I want something different than what others may include as well as going more with my favorites over stronger Pokémon too.