In my opinion I think it was because Regigigas would of been too over powered without Slow Start. If you compare it's Stats between other Pokémon in the Ubers tier you'll see where I'm coming from. Note I am not going to compare Regigigas with Pokémon released after it as I am explaining why they might of done it at the time.
Special Attack: 80
Special Defence: 110
When Regigigas was released it had the second highest Attack Stat, second only to Deoxys Attack Forme at a whopping 160. Regigigas's Attack Stat was even higher than Groudon, Rayquaza and Deoxys Normal Forme. It's Speed Stat was also relatively high, even though it wasn't the highest it was still higher than Ubers such as Ho-Oh, Groudon, Kyogre, Rayquaza, Dialga, Giratina and Deoxys Defense Forme.
When Regigigas was released it also had relatively high HP, Defense and Special Defense at 110/110/110 respectively. At the time there was only really Lugia, Giratina and Arceus that were considered better than it in all aspects in a defensive role. Although Lugia and Giratina had more weaknesses and Lugia did not have Multiscale, as Hidden Abilities had not been released yet. As a Normal type Regigigas only has one weakness, this being to Fighting type moves.
At the time of it's release if Game Freak hadn't give Regigigas Slow Start it would have been too over powered. With only one weakness and high Stats it could demolish pretty much anything. To counter this I think Game Freak wanted to nerf it's power but instead of decreasing it's Stats they give it Slow Start probably so Slaking wasn't the only Pokémon with a hindering Ability. This follows through into Generation V where Archeops is the Pokémon that has a hindering Ability.
Hope I helped :)