I use some customized hotkeys fairly often - the q,w,e,r,t set for manual casting of abilities 0-4, the a,s,d,f,g set for toggling autocast on abilities 0-4, k & l for dock/launch strikecraft. And band-boxing + tabbing is useful for catching moving units... I can never catch them by trying to click on them, esp. strikecraft and vettes. As for planet/econ control, that's basically entirely clicking for me, since the planet control card is good enough.
What would be nice is some way to alter unit behaviour. There is an old old now-freeware RTS called Warzone 2100 (http://wz2100.net/) which had groups of units led by a commander unit, slightly similar to fleets in SoaSE, with various tactical management options for the whole group (firing ranges and behaviours, etc.). But one of the options that I really liked in WZ2100 was the ability to set units to auto-retreat to the nearest repair station after taking a certain % damage (75/50/25), and so they would automatically try to fall back after getting damaged to that point, get repaired, and then automatically move to rejoin the commander. The pathing was bad and if the commander was damaged the whole group would begin to flee haphazardly, but the idea was very nice in my opinion.
Presently in Sins, retreats are manual and in fleet battles generally only capital ships and titans are pulled out manually because of their value - frigates and cruisers of course have no self-preservation automatic behaviour and fight to the death. It would be nice to be able to set 'retreat rally points', possibly around a Repair Bay or Temple of Renewal or Starbase, and hence set units to fight, say, until shields are down / hull at 75/50/25% (or fight to the death) before they automatically retreat, and then regenerate to a set amount (say full hull, shields to 50%, full shields - some customizable option) and automatically rejoin. I think it would lead to an interesting set of tactical choices - you could have your Hoshikos/Overseers present in the battle, where they're vulnerable to an attack, and set your units to fight to the death because they'll be healed while they're fighting, or you could have your healer group act as a forward mobile repair rallypoint. If you don't have such units, then you'd have to watch out because the enemy could flank you with a group of corvettes and pick off damaged units as they try to make it back to your designated rally point. TEC Rebels could have damaged units retreat into the protection of the pirate base. And you'd have to set your frigates to choose whether it's worth breaking formation to pursue and kill a fleeing unit (which is probably how corvettes and strikecraft would behave) or maintain formation and fight on (probably better, for, say, Illuminators). And unlike the clunky, dopey commander units from WZ, Sins could have a fleet have a first, second, third, fourth-in-command, etc. group of ships in a fleet, so that if one of them retreats, the flagship becomes a different ship until the original higher-ups rejoin.
Another unit behaviour feature that has been requested by people before would be the 'alt-attack', to set a group of units to prioritize attacks on a certain type of enemy unit on command - say, getting corvettes to prioritize bombers, or fighters to prioritize LRFs. I would support this idea.
Edit: And another thing regarding unit behaviour - it would be nice to preset a certain unit type's default starting behaviour from somewhere, inside or outside of an actual game. So that you can make Guardians come pre-built with Hold Position and all autocasts turned off, have carriers come pre-built with fighters and bombers already queued up, etc.
So this is all stuff that would be nice to see in a Sins sequel, whenever if ever that comes out. The original Sins is too.. entrenched by now, and is a brilliant game, but of course isn't perfect and has room for improvement!
Also, agreed about the Coronata. I love Unity Mass, esp. combined with Malice. It looks and sounds awesome and has awesomely lethal effect. Suppression Aura is neat too, as is Repossession. I personally don't tend to put points towards Subjugating Assault though - I like a more pure combat-oriented style with lots of antimatter dedicated to Unity Mass blasts. Probably the Coronata's biggest weakness would be vulnerability to bombers, which all Titans have, but is most so for the Coronata and Ragnarov. So Halcyons with Telekinetic Push and Aerias and lots of fighters are its friend, as are Dominas for help against Phase Missiles. Doesn't synergize very easily with the Guardian though - you need to position them to Repulse enemies into the Suppression Aura, which is a bit tricky, and a badly-timed/badly-positioned usage or Repulsion can just as well nullify the benefit of the Aura.