Regarding the "Heroes on both sides" thing-the comics actually get into this a bit. There was a story arc recently called "Hero Of The Confederacy".
There's also a deleted scene from the movie where the motivations for the Seperatists are made a bit more clear. It's between Anakin and Padme being captured in the droid factory and the arena scene. Here is the script excerpt:
NT. GEONOSIS, CONFERENCE ROOM - DAY
Count Dooku sits at a large conference table with Padmé on the far side. Anakin stands behind her with four Geonosian guards standing behind him. Jango Fett stands behind Count Dooku, and six Geonosian guards stand behind him.
Count Dooku
We don't recognize the Republic here,
Senator, but if Naboo were to join our
Alliance, I could easily hear your plea
for clemency.
Padmé
And if I don't join your rebellion,
I assume this Jedi with me will also die?
Count Dooku
I don't wish to make you to join our cause
against your will, Senator, but you are a
rational, honest representative of your
people and I assume you want to do what's
in their best interest. Aren't they fed up with
the corruption, the bureaucrats, the
hypocrisy of it all? Aren't you?
Be honest, Senator.
Padmé
The ideals are still alive, Count,
even if the institution is failing.
Count Dooku
You believe in the same ideals
we believe in! The same ideals we
are striving to make prominent.
Padmé
If what you say is true, you should
stay in the Republic and help Chancellor
Palpatine put things right.
Count Dooku
The Chancellor means well, M'Lady,
but he is incompetent. He has promised to cut
the bureaucracy, but the bureaucrats are
stronger than ever, no? The Republic
cannot be fixed, M´Lady. It is time to start over.
The democratic process in the Republic
is a sham, no? A shell game played on the
voters. The time will come when that cult
of greed, called the Republic will lose
even the pretext of democracy
and freedom.
Padmé
I cannot believe that. I know of
your treaties with the Trade Federation,
the Commerce Guilds, and the others,
Count. What is happening here is not
government that has been bought out by
business… it's business becoming government!
I will not forsake all I have honored
and worked for and betray the Republic.
Count Dooku
Then you will betray your Jedi friends?
Without your cooperation I can do
nothing to stop their execution.
Padmé
And what about me?
Am I to be executed also?
Count Dooku
I wouldn't think of such an offense.
But, there are individuals who have a strong
interest in your demise, M'Lady. It has
nothing to do with politics, I'm afraid. It's purely
personal, and they have already paid
great sums to have you assassinated. I'm
sure they will push hard to have you included
in the executions. I'm sorry but, if you are not
going to cooperate, I must turn you over to the
Geonosians for justice. Without your
cooperation, I've done all I
can for you.
Jango Fett
Take them away.
There's also a deleted scene from the movie where the motivations for the Seperatists are made a bit more clear. It's between Anakin and Padme being captured in the droid factory and the arena scene. Here is the script excerpt:
NT. GEONOSIS, CONFERENCE ROOM - DAY
Count Dooku sits at a large conference table with Padmé on the far side. Anakin stands behind her with four Geonosian guards standing behind him. Jango Fett stands behind Count Dooku, and six Geonosian guards stand behind him.
Padmé
You are holding a Jedi Knight,
Obi-Wan Kenobi. I am formally requesting
you turn him over to me, now.
You are holding a Jedi Knight,
Obi-Wan Kenobi. I am formally requesting
you turn him over to me, now.
Count Dooku
He has been convicted of espionage,
Senator, and will be executed.
In just a few hours, I believe.
Count Dooku smiles.He has been convicted of espionage,
Senator, and will be executed.
In just a few hours, I believe.
Padmé
He is an officer of the Republic.
You can't do that.
He is an officer of the Republic.
You can't do that.
Count Dooku
We don't recognize the Republic here,
Senator, but if Naboo were to join our
Alliance, I could easily hear your plea
for clemency.
Padmé
And if I don't join your rebellion,
I assume this Jedi with me will also die?
Count Dooku
I don't wish to make you to join our cause
against your will, Senator, but you are a
rational, honest representative of your
people and I assume you want to do what's
in their best interest. Aren't they fed up with
the corruption, the bureaucrats, the
hypocrisy of it all? Aren't you?
Be honest, Senator.
Padmé
The ideals are still alive, Count,
even if the institution is failing.
Count Dooku
You believe in the same ideals
we believe in! The same ideals we
are striving to make prominent.
Padmé
If what you say is true, you should
stay in the Republic and help Chancellor
Palpatine put things right.
Count Dooku
The Chancellor means well, M'Lady,
but he is incompetent. He has promised to cut
the bureaucracy, but the bureaucrats are
stronger than ever, no? The Republic
cannot be fixed, M´Lady. It is time to start over.
The democratic process in the Republic
is a sham, no? A shell game played on the
voters. The time will come when that cult
of greed, called the Republic will lose
even the pretext of democracy
and freedom.
Padmé
I cannot believe that. I know of
your treaties with the Trade Federation,
the Commerce Guilds, and the others,
Count. What is happening here is not
government that has been bought out by
business… it's business becoming government!
I will not forsake all I have honored
and worked for and betray the Republic.
Count Dooku
Then you will betray your Jedi friends?
Without your cooperation I can do
nothing to stop their execution.
Padmé
And what about me?
Am I to be executed also?
Count Dooku
I wouldn't think of such an offense.
But, there are individuals who have a strong
interest in your demise, M'Lady. It has
nothing to do with politics, I'm afraid. It's purely
personal, and they have already paid
great sums to have you assassinated. I'm
sure they will push hard to have you included
in the executions. I'm sorry but, if you are not
going to cooperate, I must turn you over to the
Geonosians for justice. Without your
cooperation, I've done all I
can for you.
Jango Fett
Take them away.