The freighter unload thing is a known issue:
http://aurora2.pentarch.org/index.php?topic=10637.0You can easily see which ships need an overhaul in the logistics report tab in the naval organisation window, sorting by time since overhaul. Similarly, you can sort by deployment times. Information in this screen is colour coded so it's easy to see at a glance when something needs attention.
You can set a conditional order to overhaul, but the conditions are a little limited at the moment and the % supply conditions are still buggy so I wouldn't rely on these to reduce the amount of management of ships.
Part of ship design is how much micro you're willing to do. Fighters and carrier ops are very micro intensive at the moment, especially survey carriers, while a big-gun/high endurance cruiser based build the least (although it's arguably harder to design effective beam warships). How many years of maintenance and deployment are you building your ships to have?
My exploration ships, for example, typically have a four year deployment time and five years of maintenance so there's some lee-way. Everytime they overhaul the crew gets their deployment reset. Military ships are designed for a year away from a base of operations, since they spend most of their life at a fleet base.
With managing multiple colonies, are you using civilian shipping to move installations? You trade control and speed for less management if you just set, say, earth to provide 1000 mines and request mines at your colonies as you need them. Are you using repeat orders for infrastructure and colonists? I like to build colony ships with both cargo bays and cryos so I can just set them to pick up infra and colonists and forget them.
We are missing the 'repeat orders x times' function from VB6, which I hope will come back.
Also, it's worth bearing in mind that there is no 'win state' in aurora. There's no incentive to play efficiently or pay attention to everything all the time. The game will warn you if you have unassigned labs and if your ships are falling apart, which are the most important things. Centralise production onto a handful of 'forgeworlds' if you don't want to manage loads of production sites.
If you want some inspiration as to how to manage/build large empires, I recommend Haji's from the ashes campaign (
http://aurora2.pentarch.org/index.php?board=168.0), where he played three different races with different empire set ups: one super spread out, one super centralized, and one somewhere in the middle.
Edit: I'll also point out that the faster speed of C# might be making you feel there's more management to do all the time. In VB6, where mid-game it was taking something like 30-60s to process 5 days you often didn't have to stop to do things often in real life time terms. Now the player spends more time managing things, just because the turns process faster. Once you have a decent sized empire up and running, maybe drop from 5 day turns to 1 day turns to relax the game pace a bit and just enjoy watching your empire function.
Edit 2: Dont' forget to queue up production and research orders. Ship refits can also be queued up now as well.
Edit 3: Sorry, just remembering possibly useful things as I play. In case you weren't aware, most drop down menus in the game can search the option you want. For example, in 'select name' in class design. If I select the leftmost column and press 'u' on my keyboard it will jump to UK prime ministers, which saves me scrolling down there. This works on most tech design options, the research drop menu, and a few others I'm probably forgeting. The scroll wheel on your mouse will also scroll drop menus too.