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.