Koishi's biggest problem is that low speed (for a sweeper), and it is coupled with a terrible special defense (although she can take physical hits reasonably well). She is thus best used with Light Screen support, or with Baton Passed Calm Minds, Mana Charges, or Agilities (No Touhoumon with Amnesia can pass it on, unfortunately).
Magical Leaf is there to hit Suwako with 240 base power, as Suwako resists Fire Blast and Ice Beam, is immune to Thunderbolt, and shrugs off Signal Beam (which is Special if you are using a patch with DP mechanics) with her 110 base special defense and decent HP. It also hits some ground types in harder than the other three moves would, and even if it happens to be as strong as Fire Blast when 2x effective, it has valuable consistency over the said alternative. Remember that Koishi does not get any form of STAB on all her best attacks, so that monstrous special attack would actually play out to be weaker than you think.
As mentioned before, Signal Beam is an option for those who play with DP mechanics, as it allows Koishi to do higher damage to some Darks and Psychics, but it makes it impossible to beat Suwako without being KO'd by Surf first. Flamethrower is a more consistent alternative to Fire Blast, although it is less powerful and you may have difficulties OHKOing some of the bulkier touhoumon, such as Kanako. Do not bother with Super-ego, it is just Disable, and Koishi has no business disabling enemy moves when she should be ripping things apart with special assaults.
Timid is suggested over Modest due to the difficulty of setting up a Speed pass. (The only touhoumon capable of passing Agility, or even Tailwind is Lyrica, who is extremely fragile).
You can also opt to use Blizzard and Thunder, but they have a very high chance of missing as The Computer Is A Cheating Bastard... though with save states, you can cheat and spam them until they hit.