Who do you think the 'good' guys are? Resistance or security?

Depends on how you look at it, and what your moral and ethical standards are. Personally, I believe the Security are the good guys, mainly because I have high moral standards, and the Resistance have done questionable things morally and ethically.

Security. Obviously.

Chen could be considered a bad guy, some of the Founders might be bad guys, some of Security are probably bad, and some of the Resistance are probably bad. The tricky thing about wars are the moral greys involved, one side won't be evil, it will be individuals and small groups composing the minority of both factions that could really be called "evil."

This is exactly what SD wanted from the start. They didnt want the story to be completely 1 sided much like EVERY OTHER SHOOTER (except for the odd 1), they wanted there story to be compelling though this didnt exactly happen. Im glad to see the story coming up alot on these forums lately im glad to see what ppl think of SD concept.
I personally wouldn't side with either side on this 1, there main problem is that they both have extremists in command on both sides.

Im a bit biased towards the Resistance because of the drive to equalize the Ark.

You could consider this, up until the Resistance starts trying to blow up major parts of the ark. (Founder's Tower) And all of a sudden they've fallen dead into extremism and are essentially bad guys. While their initial goals and means can be seen in a good light, their actions are bad, and get worse as the games goes on.

There are only bad guys.

"War makes fascists of us all"

Neither. They did a good job of blurring the lines with both sides hiding information, taking things too far and misleading their soldiers. Of course at a quick glance it's easy to pin Resistance as the bad guys due to some of the extreme actions they take and today's view on terrorists but Security has their faults too, they just aren't as obvious or attention grabbing as the Resistance's desperate actions.

A very small minority hold all the wealth while the vast majority are rationed supplies, used as free/cheap labor and live in rusty slums. Because of that I agree more with the Resistance's cause of equality, but not their actions.

Emerald sums it up very well, because the actions are difficult to accept.