Auto-attack causes the ships to go after the ones they have the best damage bonus, then work their way down from there (example, Heavy Cruisers go after LRFs first, since they the highest bonus to damage when attacking them). Reading the infocard on each ship in the construction menu also shows what they are most effective against (carrier cruisers read none since the carrier has no weapons of its own and support cruisers read none since they aren't meant for direct combat).

Ships perform most efficiently when you micro their abilities yourself. There's little more frustrating than seeing 4 or 5 Subverters perform Distortion Field on one target, since only the first one works and the effect ends when that first cast expires. Leaving abilities to autocast does get the job done, but less efficiently in terms of ships and cost.

From what I've seen on the forums and from personal experience, a well balanced fleet usually performs best (which pretty much can be said for any race). In the case of Vasari, its good to keep quite a handful of Overseers to prolong the lifetimes of your ships and Subverters to hinder the enemy.

Consider capitals as ships that enhance a fleet, not as a one-ship fleet (using them as such usually results in a spectacularly exploding capital). That said, 16 capitals generally isn't a good idea unless you're looking for the max capital ships achievement, since you're using 800 out of 2000 max fleet supply for them. Given that siege frigates fare rather poorly in terms of both durability and fleet supply usage, you'll definitely need a few capitals around to do planet bombing (in particular the one that specializes in planetary destruction (Marza/Revelation/Vulkoras)).

I'm a Vasari player too so my suggestion is to mass assailants and enforcers, but also comined with overseers and subverters. Another good idea is to have a fair ammount of flack frigates. As said before siege frigates are not durable and quite expensive for their duties. I would only build those when planet defenses have been eliminated and I need to take out the planet, but still I only build five or six. The skirmishers are also a great Idea as they have a surprising ammount of shield and armor for their size, these are great meat shields. You might also want some carriers forthe Vasari squadrons are small in number are in fact quite strong.

For Capital ships I wouldn't make them a top priority untill later. And my maximum cap ships that I build is 5 or sometimes 6. The important thing is not to depend on them. Cap ships are considered as support ships and les as weapons of mass destruction. Some cap ships you might want to pick up on is

1) Jarrasul Evacuator: Great ship it can colonize planets and has the nanite ability which can eat through anything in it's path, the drain planet ability is a worth while investment for it as it does massive damage and gives you free stuff.

2)Vulkoras Dessolator: I build about two of these for their super strength and the ability to take out a planet all by itself. This is both an effective combat ship and planetary bomber. It's sige platform ability is very usefull at destroying enemy planets and it renders the siege frigate obsolete.

3)Antorak Marrauder: It is a good all around ship with a lot of usefull abilities and is the fastestr capitol ship in the game although fast it is its weapons lack power, this is a support ship by far.

4)Devastator: A very powerful ship but it's abilities benefit it more than your fleet but this thing is indeed a fierce fighter with great potential if used right.

For Abillities I would micro them it just makes your fleet like three times more effective. The thing is to use an ability at the right or wrong time can mean victory or defeat. The auto manage is okay but will not be as effective as microing. You know what they say a machine is only as smart as the person who built it. Hope this helps.