Well you could mod the ships so that they don't auto-join fleet.

And to be honest, I don't really use the fleet functions that much, I rather use the groups 1-0 instead.

I often use 'fleets' so that new ships adopt specific behaviors when they join the rest of the group. For example: I have my fleet in a enemy well with heavily defended structures all in a ball. To prevent new ships coming into the well from wandering over to attack the defense ball, I'll select my cap ship and create a fleet and then set the cap ship to 'hold position'. All incoming craft will join the fleet and hold position, and I wont have to tell each one to do so.

Fleets are really clumsy to maneuver, especially if there are a lot of things to run in to. They spend most of their time "reforming" anyway.

The best use is when your navy is chock-full of support ships and you want them to keep their relative place to help the frontline ships during combat.

Oh and you can turn off the auto join fleet command by right clicking on it

To be honest, I rather see in the next expansion is to create the ability to move in a general direction instead of having ships move and then go back into formation and then have to move out again just to attack

I disband them, that's what I do.

I guess fleet really isnt a useful Thing i guess.

I have to agree with deveiver in this point, fleets are exactly good for the things they offer: Adapting the fleet settings for each single ship in the fleet.

1. joint jump: when attacking a strongly defended enemy planet its quite handy when all ships arrive together. much better than having all your LRFs jump first and die in enemy fire before the cavalry arrives

2. fleet cohesion: what good do Hoshikos (for example) do if the ships they shall repair are spread over the whole grav well? 

3. hold position: when encountering a fully upgraded SB its probably your wish to let your bombers do the work and keep the rest of the fleet out of range. thats what "hold position" can do for you without having to micro each ship.

perhaps a global setting where you can actually set your jump % from 50 on to 100

Fleets are one of the Devs favorite features, I wonder how they use them. Maybe we're all just doing something wrong.

For me, only point 2 has any merit. Points 1 and 3 are easy enough to achieve by simply grouping ships via the ctrl+ 1 - 9 method. Personally, I just don't use the fleet option. I tend to group-jump my cap ships in a few seconds earlier than the rest of the fleet to "clear" mines and draw enemy fire.

Fleet cohesion is the only reason to use fleets and that really only comes into play late-game when there are too many ships to micro support to.

It's generally easier to just group them and move them that way, no reforming to waste time.

An advent fleet (for me) is just about alway set to hold position in tight formation, let the strikecraft horde kill everything, then send in the ships to mop up...

I've noticed that if I have flak frigates in just a numbered group, and tell the group to attack, say another capital ship, the flak frigates will move up to fire at the capital ship instead of at strike craft, and support vessels like robotics cruisers, guardians, etc. won't stay with the rest of the group, which essentially renders them useless.

With the ships set as a fleet, the flak ships only assault strike craft, guardians stay with the fleet, protecting it, and light carriers stick to the back where they're less likely to get destroyed.  Seems pretty useful to me.

To be honest, I never seen any difference when it came to tight or normal or even scatter formation, but then again, my ships were moving...