There are almost always ships at every planet, how many determined by what it is, and if its colonised.6 scouts have the combined firepower of a pea-shooter. If the planet has 2 Heavy cruisers, then you can expect your scouts to be trashed. Even the combat frigate wont do so well, except in bigger numbers.Everyone varies as to starting tactics, but I build 2 scouts first off and have them find the nearer planets with manual direction, always jump again before they can sustain too much damage, then build the free capital ship. I usually then build a second cap ship, and let them clean out the lightly defended planets. Thay may take damage, but they repair, so thats not an issue as long as you dont lose one. But before tackling a colonised world, I go for heavy cruisers to escort them. If the ai already has hangers, then you need some flaks as well. To get the heavy cruisers tho, you need at least 4 planets to have enough research for them. Dont bite off more than you can chew. Have your scouts scout, not fight. Then you know the force you need to take each planet, and can build them before attempting them.
Sounds good. I guess I'm just using the units incorrectly. So far I haven't played a game long enough to have actually researched any ships past the original 3 you get (the scout, frigate thing, and the colony ship). Mostly due to just playing for a while to get used to how things work.
I'll try research some military techs and building some better ships, and let the scouts just scout planets out, as you suggested

This also explains why scouts don't have "auto attack" on by default. Because I kept setting them to auto attack, wondering why they came out with it off... They're not really meant to - huh? I had kind of figured they were footmen in Warcraft, or something, your first basic unit. I should probably look at this game more like Civilization or Gal Civ 2 than I should as a Warcraft type game.