...Champions...
Hummmm yeah sooooooo, I've stopped playing with champions, but I can see how you see things different with them since they are free, extremely strong, replace a bunch of startships on their own, and when doing missions unlock another couple free planets worth of resources/energy/knowledge and ~50 inexpensive starships...
As for riots I had to unlock mk3 with gravity since i was vs blade launchers, and losing a couple of those is extremely expensive!
I don't actually play with Champions. I was referring to the ability to save and apply designs for all modular ship types, which make riots more convenient to retask.
Admittedly, Regen golems do skew my results moreso, but that aside, I'm not fleetwiping nearly as often, except when (big threatball) forms up outside a chokepoint on an X map.
If you've got a single checkpoint and the corresponding fleetwipe that causes, try this:
Load your fleet into (assault) transports. Send those transports in under cloak to the limits of the deployable zone of the system. Unload them, and fly even further out, to the 'incredibly slow zone'. This works best if you have bombards, engine damage, snipers, cursed golems, etc.
If you don't have said extreme range, fly empty transports + cloakers into the system, and move them opposite the enemy fleet. Move your ships (with all important Riots) into the AI system and group move away from the incoming horde towards your transports. Since this is just a threat pile and not a strike force, you should be able to do a surprisingly good job of spreading out the enemy forces in hopes of defeating in detail. If you reach your transports, judge whether to continue with the killing, or bug out.
Option 3: I find I play this game too slowly. In an effort to encourage promptness on my part, I've put a timer in the form of Spire Civilian Leaders. This has transformed warheads from a bad idea to a net gain. If I save a half-hour, I've saved roughly 5 AIP, or I'm making it back up in the long run.
If you're faced with gigantic patrols:
Rarely: EMP Warheads.
Often: Beachheads. A fortress + missile turrets can defend itself against Zombards and bombers, while your fleet stays nearby for repair and more firepower.
As Tech says, however. I find myself playing slower than I should, perhaps, which explains a lot of my refleeting. I only really hurry up naturally in co-op, though I'm always trying to make myself a quicker player by lowering the losses suffered and trying to be a bit more ambitious.
I do sometimes end up with those 'huge swathes of territory' and gigantic threat balls waiting outside, and then I suffer from fleet wipes. I'm experimenting with things though, and doing much better at least on tackling regular systems.