Glad to hear you are having fun. Lot of valid issues you brought up, all of which we are looking into. Without getting into the full details, here are just some quick responses.
"Diplomacy with the AI is still a bit odd": yep, we agree - you will be able to give gifts without the agreement and you will have a way to view their opinion of you.
"Capital Ships need to take longer to build and have higher costs": partially fixed in the next patch and our new stats collecting system for multiplayer will help narrow down the exact costs and build times.
"Fighters seem mostly useless in large ship fights": Not if the enemy has bombers or LRM's. Fighters will rip them both up, otherwise they are flak frigate fodder.
"Crystal production seems to be a huge bottleneck": New map nodes will help alleviate this and the research subjects are improved in the next patch.
"Research tree needs to allow easier access to new ship designs - else people will just go for capital ships like I did": Not so easy in the new patch and if you go all capitalships a human player (and an improved AI) will decimate you.
"Research in the tutorial implied you could research multiple upgrades at once": The game is changing faster than we can update the tutorials so we stopped updating them until the game is near done. Research is now sequential.
"Think this is already a known issue that the AI builds lots of frigates and little to no capitals": Work in progress, should be somewhat fixed in the new patch.
"More movement in combat": Maybe. We always debate this one.
"Bounty system didn't really seem to have much effect in my game": That's good, in the previous version it had way too much of an effect. We rewrote the whole system for the next patch based on feedback, hopefully we strike somewhere in the middle this time
Autosave duration can be modified by using notepad.exe to open the user.setting file in one of the following directories:
XP: C:\Documents and Settings\username\Application Data\Ironclad Games\Sins of a Solar Empire\Setting
Vista: C:\Users\username\AppData\Roaming\Ironclad Games\Sins of a Solar Empire\Setting
Change AUTOSAVE_INTERVAL 300 to the number of second you would like. Save games are much smaller in the patch (though I haven't added that to the change log yet).
Enjoy and thx for the feedback!