It's reason.

Anyway, have you tried using the civilization manager governers and waypoints to co-ordinate your ships?

I find that helps a bit, but I still have trouble co-ordinating them myself.

I usually use two waypoints close to the border of my next target. One for troop or spore ships and on for battleships. The area you pick should be easy to defend. That means there should be one or two planets that can build ships quickly and some fast military ships that can take out an unexpected threat.

When you have enough troop ships to invade all the planets you want and an appropriate military to take out their defenses, go in starsystem by starsystem. You might split your force in two or three battlegroups consisting of one main and one auxillary fleet and enough troops.

You dont have to take out all their fleets. Just keep out of their range and concentrate on clearing planets.

Don't forget to build and send reinforcements to fill in for your losses.

I like to set a rally point near the center of my territory and name it 'Central'. As I expand I add rally points closer to the border and name them using either a cardinal direction or an enemy empire like 'South' or 'Korx'. I always set them to fleet rally points so they gather the ships, but never to autoattack, I like to control when they leave. I try to set them in between several systems, and gather the ships from the surounding systems to each local rally point. I don't have separate ones for troops and combat ships. I like to have at least a few escorts in with my planetary assault fleets. As fleets attrit from either combat or deploying troops, I recombine them into big fleets again. Always attack in mass (one of the nine priciples of war).

That's a really good tip.

I've been playing a really good game today where I've had to fight three defensive wars. I will usually just put a rally on the influence border between me and an opponent/potential opponent.

However, if they're in my space, I will try to put a centralized one in between my major ship producers, have my ships fleet up there and then send them out in waves.

Also, I will usually make up three different kinds of ship for each hull size I have available. (aside from tiny, if I make these at all I'll only make one kind)

They will usually be a slow but heavily armed and defended ship which I like to call a tank (usually for sitting on top of planets), a quite well armed ship with an engine or two for general fighting and finally a lightly armed but stupidly fast ship for intercepting transports or scrambling to planets that are about to be invaded.

For cargo hulls, I will make a fast transport, a faster and longer distance freighter, a fast constructor and a fast ship loaded up with sensors.

I will sometimes obsolete some of the older models of my ships depending on my industrial strength. (smaller ships are cheaper, so I may keep them around if there's a chance I need one fast)