If you are just pushing small groups around, you can Shift-Click the ships. This lets you give the orders to all of them at once, without bothering with a fleet.
In a simultaneous game, the only thing you really need fleets for is to share supplies. And to manage 50-300 ship battlegroups
Some things to try:
- Wait another turn before making your fleet
- Reuse pre-existing fleets
- If you've got vast numbers of small fleets already, disband one first.
- Send the savegame (and a link to the mod) to Aaron.