There is already a way to do this.

When you select more than one ship, note that one of them will be the "primary selection", and have a slightly brighter selection square around its icon.

If you hit TAB, the primary selection will cycle through all of the ships you have selected.

If you form a fleet from your selection, the primary selected ship will be the flagship.

The way I usually do it is just to select the ship I want to be flagship, hold down shift, add all the other ships I want in the fleet, and hit the form fleet button.

If you somehow get it wrong, you can fix it simply by selecting the fleet, hitting TAB to cycle to the ship you want to be flagship, and hitting the form fleet button again.

Easy.

As for the sidebar scrolling, it drives me INSANE. I really hope they fix that soon.

Need more control on movement, I zoom in and out and i find i left the dam gallaxy, have to try to find where i was or click on the planitary system and try to zoom back in. Not enough controls in system, movement up, down, or side to side can not all ways get angle i want. Also ships and planitary buildings too small. by the time i zoom all the way in to watch battle, i have to unzoom to find the next enemy. Need better AI, One ship will engage you while the rest will try to move up. If this was real, the enemy would hold back intell all were with in range and then move up to fight you. Also enemy will not retreat from a fight even if out numbered ten to one. The only vessle in the hole game that will is a scout, but that just becase he moing on to the next planet. Need mines, you should be able to mine the lanes so if enemy ships are jumping in they will get hit before they enter range of the planet or buildings. Its an idea. Also need better weapons/armor/crew training/hit ratings. (If a new crew fire at the ememy it should be a one/ten chance of a hit at max range and a five to ten at close range. More exp better odds. If you shot a Main weapon at an enemy ship it should do max damage if it hits. All weapons have Pros and Cons, but this game the main weapons hit every time, but does little damage. I can kill an ememy ship with smaller vessles faster then having three battleships. Something wrong their, dont you think. More use of Fighter bombers/more hanger space for more units. I can use fighters and bombers and the enemy does not even shoot at them. More tax money, I normaly have no money, but plenty of metals and crystals. All so need more unit credits, their should be no max on how many ships u can have small or big, if u got the credits you should be able to buy more. More slots for buildings u can build next to your planets. Can not stake claim to some areas, Example (Area with no planet or big Ast. Can build meneral or crystal buildings, but thats it. Make up grades to were jumps are more faster. Sould have made it to were u dont have to colinise the plant, instead turn it to a mining planet, farming colony, or get water from planet if its more water then land. Just an idea. More use of steath attacks or mutiple attacks from diffrent directions. (Use of ast to hid your ships in to wait for an enemy attack force to move by, then move your forces in behind so they are boxed in and have to fight to get out.) I have more but thats it for now.