1. At one point I had 3 NPC (heros) who had the prestige ability. It says gives +1 to cities. I noticed that the cities still only had 1 and 2 so I thought I had to station the units in the cities. Still no change. Is this a bug or am I missing something. Also, do you have to station the heros in cities or are their effects global?
I think I remember hearing that the prestige abilities have a slight bug, but it should work on your Sovereigns, as my Sovereign has the Prestige bonus for the royalty trait, and all cities I built always started with 2 prestige. Also, to get the bonus of whatever trait they have, they do not have to be city unless it's actually specified. For example, if one Hero gives a bonus to production while in a city, then you should station him in a city that has good metal production.
2. One game I had in the store an item called a travellers cloak. I thought it ran out of stock but it turns out that only my MALE hers can see it. My FEMALE ones can't. Is this a male only item or is it a bug?
I've only tried Male Sovereigns, so can't really help with that, it most likely may be something that was overlooked that could be fixed in coming patches by Stardock.
3. I found out how to upgrade the settler units with more moves, armor, etc. But is there a way to upgrade the Caravan units to help them move faster, have more armor or are we stuck with the 1 (I don't see the unit on the upgrade units screen). Is this a bug or the way the game is.
Don't think that's possible for caravan units, or it may be based on a specific research tree within the Warfare line. (Keep on checking the line that opens up additional packs, like regen kits, etc..)
Well hope this helps