Haven't had time to read them in detail yet.
Though a few things that a quick read-through didn't make clear to me or at least seemed inconsistent:
I believe one hero (spy?) has the ability to reveal heros. In another point you say heroes must be placed on the vehicle they are on. Did I read this correctly?
I don't think you're looking at the latest version. In the present iteration, the Spy can assasinate.
The heroes seem to have very differerent power levels, some granting always +4 bonuses, others just revealing information or having a limited chance to affect a ship once.
Oh yes. Not all Heroes are equal, just like not all ships are equal. Some of them are better to have than others. Although they've all been severly rewritten in the current version (they get their own initiative now and take actions just like a ship does). Plus they can level up.
What are the cool uber-features of Shadows/Machines that they have so few heroes? Do you just expect them to have very powerful craft and Heroes exist to compensate for that?
It's a flavour thing. These guys rely more on technology than individuals. The game's purpose is to reflect the factions it is representing; the Shadows or the Borg, for example, never had plucky pilots, bold captains, and the like.
Balancing out sides for fair battles is going to be a challenge, but it's one of the initial design concepts I am determined to retain - no arbitrary standardising balancing factor which takes away the exception-based flavour. It'll be fine for published scenarios, as the designer will be expected to design a balanced scenario, but at some point I am going to need to work out how to make it easy for players to do so, too.
I suposse a "Assimilate Hero" ability might be in order for the Borg-equivalent. (Destroying a squadron or ship with an hero aboard assimilates him?).
There's already one. At least, I think I put it in there under the Hive ship (its boarding parties can do that). Transfers the Hero to the Hive player's countrol.
Should there be a Psion/Telepath hero? (The Corps is Mother, the Corps is Father

).
Absolutely (also think Deanna Troi). I have a half-dozen more Heroes in mind, although I intend to save them for an expansion. For example: Medical Marvel (a doctor who can restore a dead Hero back into play), Red Shirt (can take the place of another Hero's demise), etc.