Actually, some of those would be better with a Timid nature. Without a Timid nature for Alakazam, it loses to base 115s. Kyogre prefers a Timid nature for its Choice sets along with the Sweeping CM set but prefers a Modest one for more bulkier sets. Manaphy wants Timid to outspeed base 90s, while Timid/Naive Magnezone beats Metagross and Breloom by 1 point. Latias needs Timid as well in order to speed tie with other Latias.
In reality, the only Modest Pokemon that jumps into my head is Sub Petaya Empoleon, and even then you can use Timid to outspeed Choice Scarf Timid Rotom-a. The metagame is way too speed based to be using Modest anymore.
Modest Kingdra on a Rain Dance team :P