I'd like to see some rescripting of auto-cast behaviors for a number of skills. Some of the skills inherently waste themselves, or trigger at times that just aren't helpful.
This. #1 and #2 on my list to re-do are both Advent, since I'm a long time Advent fan (though I 
me some Vasari too).
- Transfer Antimatter - Don't target other Disciples. That's just silly!
- Vengeance - This always seems to autocast on self, even when other ships (like, say, Animosity'd Radiance) are taking heavy fire and the Rapture is taking none. This should find a target under heavy fire and cast on that, perhaps even wait for a threshold to be reached.
Other stuff on my list:
-Manage fleet composition (frigates/cruisers etc) like the fighter/bomber system - at the fleet end of things. Micro-managing multiple factories to do parallel construction as losses add up is not fun for me (and I suspect others). Let me link factories to fleets (as with the current rally point system) or auto-recruit factories and set my fleet composition - reinforcements will be built automatically as losses accumulate.
-You know how shift-click lets you select your own ships by class? Being able to issue targeting orders that way (ie. shift-click on enemy LRF = target all LRFs) would go a long way towards mitigating the issue of the empire tree moving ships around in combat. Also, being able to set "focus fire" or "spread fire" for groups of ships would make this really useful and cut down on the number of clicks needed to give common orders.
-Give us some way of finding out about which Artifacts other empires control (my conquests are very Artifact driven 
) or even sharing Artifact benefits through pacts.
-Make it easier to clear a gravity well of structures once a planet has been colonized, like using constructor ships to scuttle/deconstruct them. Something for minefields too... some planet-based defense should give you mine detection.
-Let me mark gravwells as "dangerous" so the navigation pathfinder will ignore them and ships will avoid them. This would really useful for stopping scouts on auto-explore from criss-crossing the pirate base and whatnot. Should be overridden if I click specifically on dangerous gravwell.
-Don't let ships I own get get hidden when zoomed out. Even if there's a huge friendly fleet at the planet where my single scout is, I still want to see a single bar with my colour on it next to the planet icon.
-Fleet icons need to show up in more places so I can click on them. If I'm zoomed out enough that I'm just seeing the planet icon I still want to be able to click fleet icons without scrolling waaaaay up the empire tree. Maybe just add them to the regular "at this planet" listings in the empire tree so they're always available!
