3) Fleets are not smart enough to separate when say the capital ship in the fleet decides to bomb the planet. In this situation, if my cap ships fleet has combat frigates/cruisers in it, they will simply sit in formation around the cap ship while the planet is bombed leaving logistics structures unthreatened. A much more sensible behavior would be for the fleet to split itself and allow the frigates/cruisers to attack the logistics structures while the capitals bombed the planet, or even better to allow the attack priorities of ships to be changed by the player in game so that if my objective is a raid, I can tell my ships to ignore the planet and destroy everything in orbit first, and if my objective is to destroy the planet and damn everything else, I can order the planet to the top of the attack priorities.
Good post! I believe the devs wanted to keep the complexity level down so it is open to all levels of players, adding the ability to control the behavior to the Siege Frigates in a Fleet that is also composed of a mix of other combat craft, which would be delegated to attacking the logistics or tactical defenses while the siege craft complete their role (belonging to the SAME fleet) just adds a new layer of complexity... not a huge one, but enough that takes you attention away from other happenings.
As a side, attention in this game is really an important point any of us need to come to grips with, the more you attention is taken away by managing your fleets, their behaviors, etc... this causes a ever widening problem for a player, depending on the size of his Empire and also the size of his fleets. The more you distract your opponent the better (i.e. black market/pirates bounties), the more you must manage your empires infrastructure then the more you will be at a disadvantage (except of course those exceptionally gifted savant-like power players).
In my opinion, the aggregation of ships roles would best be served by just creating a second fleet that is composed of siege craft (fleet #2) for example then lets say "fleet 1 - attack craft" and controlling them independently.
Do I understand correctly that you can create a nested 'fleet within a fleet'...

because this morning I was having difficulty adding additional ships to an existing fleet... inadvertently I believe I nested a fleet withing a fleet, until I removed all selected ships from the fleet and then 're-fleeted' those ships... was the nesting instead my imagination?