1.) How many hero choices should a good open rpg have? I always have trouble deciding when I have enough heroes (I have craploads of ideas for them) so I can start using units for creeps and other stuff.
If you want replayability then have at least three to four more than the amount of players to give more of a variety, and make sure each character is unique so that people will actually feel compelled to play the map again as a different unit. If not, have at least one for each player and then one that's left out.
2.) Should the players be able to choose their heroes by pressing a button, or should there be some sort of challenge involved, ie, you run a bound and you get a hero depending on how far you get, or you go to a certain place, or beat a certain enemy, etc?
I think that if people want to play an RPG then they want to have an easy selection rather than play a bound. You'd be surprised how many remakes of the game people would play through until every single person got the unit they wanted.
3.) Should the heroes be godlike (like in many noob rpgs), or should I go with a more realistic approach of making the heroes just slightly more powerful than any other unit?
Have them be slightly better than any other units, but able to earn certain upgrades throughout the storyline and make them rely on tactics and spells/abilities/skills.
4.) Should the bosses be unique, or should I recycle units by making them the same unit but with ups and spells and whatever?
It depends on the amount of enemies you want. I know I wouldn't be happy to face the same guy again, just with an upgrade.
5.) Do most b.net noobs actually pay attention to the storyline of a game?
Not really. They really just care about killing enough guys until they can upgrade everything to the highest possible amount of upgrades. If it's a map like Quests Open RPG, then they'll just buy all of the towns and try to conquer the world, then leave.
6.) Should the story revolve around one key item (ie, The Ring, a particular person, a particular place, a special tree, etc), or should the issues a player is concerned with change with each passing quest?
I like to have a main story with some parts branching off and later intertwining with the main plot. For instance, have one of the characters introduce the players to another character who will give them quests/missions. Perhaps an item can be introduced in this side-plot, like a ring. Perhaps after all of the main story missions are done, and you haven't done the side-plot yet, you'll have to do them, and "the ring" can take effect in the plot and the main story continues.
7.) Should the map be composed of water with a lot of relatively small islands, or should it be a large landmass with lakes, rivers and oceans? (In other words, do I start my slate with water and then paint land, or do I start with land and then paint water on it?)
Start off with a canvas of water and plot some patches of land.
8.) How clear should the line between good and evil be, if there is one at all?
I think in a StarCraft RPG, good and evil are just people/monsters that are hostile to each other. Yeah... in other things, good and evil have a much more clear of a line.
9.) Should each faction's towns be of a different race, or is it better to save units and make each town use the same buildings for the same purposes? (ie, should I use an evolution chamber for the "evil" town and a forge for the "good" town, or should I just use a forge for them both?)
Use different units so the player can easily depict good or evil.