New player here. I've only been playing Sins for about 3 weeks now. A friend gave me a shareware disk he got with a magazine, I loved it so much I went out and bought a copy so I could upgrade to v1.16.
Before starting this thread I did the wise thing and read through several of the forums and even did a search on "fleet" issues. And I now see that I'm not the only one having issues when trying to create fleets, especially when you're trying to do something creative like have one fleet protect a another fleet while it's being created. Hopefully some of the suggests on on how to opperate the auto join feature will be adress in future versions of the game.
I will briefly touch on a subject that some feel have been discussed to the point of beating a dead horse. And that is of fleet limits. I, personally do like the current system. I see the value of having to determine how much fleet you can afford and the limits placed there on. About the only change or tweak I would like to see, is gaining some sort of bounus points for more fleet slots as you expand your empire. Simlar on how risk operates. I just hope that someone can tell me that when I go to play the larger games I'll have the ablity to have a larger fleet then 2000 slots when I reach 75% of my income and the max of 14 caps when all is research/paid for. That's all I have to say about fleet sizes...
Fleet captains on the other hand are driving me nuts. I don't care if I'm being attacked by pirates or the AI, The captains of my Cap ships, most notibly the fleet comand ship has the stupidist capitain. When the invading fleet arrives he goes of chasing after a a fighter or something mean while giving the rest of the invading fleet time to disperce and start causing me all kinds of head aches. Unless I micro manage his ever move, This becomes ever more frustrating when the AI fleet attacks a different planet then the pirates are at the same time. I've tried every setting Sins offers and still end up having to chase after my fleet comand ship and sending him back to the more important targets time and time again. 
This reminds me of an much older fleet type rts game I use to play called Harpoon. While I don't think we need the complexety that game offered when it came to arranging ships within a fleet. I do wish there was a way to make certain assignments within a fleet as you build one up. For example... Keeping a frew robot ships near the caps to repair them, or telling the crusiser carriers to stay at the edges of a gravity well out of harms way. I would love to see some you go to build a particular ship(s) to add to a fleet some check boxes as to how or what you want them to do within the fleet. Couple a quick mouse clicks, then add quanity you desire, then click "build"...done. This could also be the way to fix the auto join issue. Give a check box to auto joing then a list of fleets pops up and you can just check off a box as to which one you want it to join, or something like that.
One thread that I read in particular that I liked, spoke of having waypoints and patrols for scout ships. I would like to expound on this ablity a bit further. Depending on how you play the game, you're most likely to have defensive and offensive fleets with cap ships. That only make sence. But what don't see the ablity to do is having smaller harassing fleets. Where you can take a few crusiers, make on the fleet leader, and send them out on raiding parties using way points to harras the enemy. Would also make the game a bit more challenging as well. Becuase the AI or other players in multi could do the same to you. You could also use these mini fleets to patrol owned territory and such as well.
And finally, I would like to note to any of the Dev's that may read this. I do realize you've spend alot of time and effort writting the code and developing this game. It shows! I absolutly love it! I have an older machine and that's still running an ATI 9600 card and I can't begin to tell you how great the battle scenes look on my system. I can only imagine what it would look like if I had more current hardware and monitor. I just have to say thanks for making such an excellent game. I really wish I knew about it a year ago when it first came out, because I've been missing out on some good game play! So, I'm going to keep an eye out for you have in store for us for Sins 2!!!! <evil grin> That I will buy on it's release date!
Jaxx