Well perhaps I'm the only person having this issue so it's not an issue at all, but certainly I didn't spot this. I wouldn't say selecting starting position is that normal for RTS anymore, you'd normally just choose between Fixed and Random without specifying a point. In AI War I didn't even pay much attention taking the map simply as a display for whether you'd like the seeding or not and the special icons to represent special events or something on the map.
Gotcha. I'll leave it for now, but we'll see what other people say.
Even reading the text at the bottom of the display now I'm left with the following questions:
1. Do the other ships remain once I pick a location?
1b. If not, why not a drop down instead of map locations?
1c. If so does the AI get the ones I leave or do they await capture?
2. What if I pick a location without bonus ships?
Everything else was well tool-tipped.
Whatever you ship type you pick is inextricably tied to the location you choose, which is is why it's part of the map and not a dropdown. There might be a really great ship type in a really bad position, or vice-versa, as part of any given galaxy map scenario. The other ship types that you don't select have no bearing on your actual campaign, they may or may not show up for the AI or through Advanced Research Stations. They are neither more nor less likely to show in the scenario.
The way the AI gets its ship types is unrelated to yours, by the way -- they might have the same types as you, or something wildly different.
For #2, you can't choose any locations without a bonus ship type. That's part of the point of what it is telling you -- here are the valid starting locations, and here's the bonus type you would start with at each location. Each of the 8 locations is likely to be a wildly different scenario, even if the map seed is the same and the overall structure of the planet links is the same (in other words, the stuff on each planet, where the AI home planets are, etc, varies by starting location as well as map seed. Also by AI type and number of players, incidentally.)
Hope that helps!