Though I love how simple the former is to write and research, I really don't think it has much purpose beyond giving the reader a bit of trivia when it's obvious that a move is nearly a complete clone of another. I'd say the latter is the way to go, but that raises the question of where exactly do we stop and say that these moves are the one we're listing as related.
A possible solution is to just restrain moves not by their type or their base power but by their purpose. As an example, I'll use Flame Charge. Since its primary purpose isn't to attack the opponent, I wouldn't even mention Flamethrower or Fire Blast, but instead mention options like Agility, Rock Polish, and Gear Shift. Since the related moves would be rooted in purpose and not similarity to other moves that may be of a different type, I think that grouping physical and special attacking moves like Earthquake and Earth Power would be the way to go since they both serve a similar purpose. We've already done this for moves like the entry hazards and it looks much nicer than listing Flamethrower, Ice Beam, and Thunderbolt everytime a move has 95 base power and an extra effect.