I've said it before, so I'll say it again...
Fleets only really behave like a fleet when you issue orders only to the flagship. The rest of the fleet makes it's decisions based on what you just ordered the flagship to do. If you told the flagship to attack some heavy cruisers, it's gonna saunter on over and do it, meanwhile the flakk ships will go "wtf? waste of time, imo." and just follow in formation shooting at fighters/bombers as they go.
Also, you have to set your engagement envelope properly... ANYTHING other than "Hold Position" will see your pretty formation fall apart as segments of your fleet break and attack based upon their range (either local or system if I recall properly).
If you want the fleet system to work for you, you need to custom tailor several fleets, and learn to micro them via their flagships. Otherwise everything disintegrates into a large furball (or melee, if you prefer).
Most the time... having a big mess and just micro-managing the capships and useful support vessels is more than enough to do the job, though. However, it's far more impressive when you do it by the numbers, and you will likely also suffer less damage as a result.
Furthermore, I have found that organizing by fleets best serves the TEC and Advent, where as the Vasari actually do quite well as a chaotic mess... but I suppose that fits with their guerilla tactics / mobility theme.
But the beauty of this game... is that you can only control a few key components of your mess, or artfully conduct fleets via flagships, or even just make a bunch of control groups out of certain ship types w/ no cohesion... and get the job done in any case.
Really, it all comes down to whatever playstyle you prefer; but imo yes, there is a point in creating fleets - it's just the way I like to do it

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Go go IC/StarDock for giving options!
-Itharus