The (Unusual) Motto
For most North American viewers, the "classic", dramatic Team Rocket motto in English is as follows (and is even part of this site's navigation at left):

Jessie: Prepare for trouble...
James: ...and make it double!
Jessie: To protect the world from devastation!
James: To unite all peoples within our nation!
Jessie: To denounce the evils of truth and love!
James: To extend our reach to the stars above!
Jessie: Jessie!
James: James!
Jessie: Team Rocket, blast off at the speed of light!
James: Surrender now or prepare to fight!
Meowth: Meowth, dat's right!
But in the episode "The Breeding Center Secret," we learn a different Team Rocket motto from the more successful duo of Butch and Cassidy:

Cassidy: Prepare for trouble...
Butch: ...and make it double!
Cassidy: To infect the world with devastation!
Butch: To blight all people in every nation!
Cassidy: To denounce the goodness of truth and love!
Butch: To extend our wrath to the stars above.
Cassidy: Cassidy!
Butch: Butch!
Cassidy: We're Team Rocket, circling Earth day and night.
Butch: Surrender to us now or you'll surely lose the fight.
Raticate: Raticate!
The Odd Thing about Jessie & James' Motto
Even though the "original" Team Rocket motto is presented as dastardly and evil, what about its actual words? Let's dissect it for a moment.
To protect the world from devastation:
This is a positive, helpful goal.
To unite all peoples within our nation:
Generally a good goal.
To denounce the evils of truth and love:
Weirdly phrased, but it could be taken to mean two things...
- To denounce the concepts of truth and love, because they're actually evil concepts in and of themselves;
- To denounce the evil things that the pursuit of truth and love can make us do.
I prefer the latter interpretation, because when we doggedly pursue ideals of "truth" and "love" without thinking about anything else, our concepts of these ideas can become skewed by our obsession, leading to later emotional hurt. So this line, in my view, is a positive goal as well.
To extend our reach to the stars above:
An ambitious goal, but not necessarily an evil one.
Team Rocket blasts off at the speed of light:
An image of adventure and strength, not necessarily evil.
Surrender now or prepare to fight:
This is the only line that even marginally sounds threatening, and it implies an equal fight rather than a certain loss.
Conclusions About the Motto

These words, though dramatic and full of flourish...aren't really evil. Jessie & James' own stated beliefs and goals, as listed above, are actually quite a bit more heroic than their presentation would lead us to believe, especially when compared with Butch and Cassidy's motto, and with Team Rocket as an organization.
So, what does that mean for them as a duo? I believe it means that we can't really call them villains--not truly, anyway. They have turned to a life of crime together, but their own motto proves how ill-fitting the garb of villainy is for them. And thus, their character development is opened further.