Hey Chipchat2,
Thanks for coming back and sharing your thoughts. When you post things like this, sometimes there are easy answers to alleviate your frustrations.
I'll give it a shot and maybe you will be more interested in continuing. But maybe not.
Resource based: You are indeed correct. However, there is no resource gathering if that makes a difference to you. You are given a set amount of points to spend which regenerate at such a slow rate that you will barely notice.
Part of the reasoning behind this was so that you, the player, can choose your army on the fly. A lot of games make you choose beforehand which units you want (and to a limited extent so does RFB) but we wanted to also have a focus on letting the player evaluate the map and enemy forces and then choose what to throw against the enemy. Also, it ties in very well with our concept of time. The more time you spend building units, the lower your score is at the end of the mission. So production becomes more of a tactical decision this way.
If none of that works, we have a modding patch coming out very soon. In it, you will be able to alter any map (or make your own) with only set armies. No production at all.
Mouse Jerky: This would be a tech help question so if you want to tell me about your mouse, maybe I can help.
Clickable Circles: The size of the circles depends on your screen resolution. Maybe lowering it would help you out.
The Flag: In order to lower the flag, you don't need to click on it. You just need to stay close enough to it. If there are no enemies nearby, the flag will lower by itself. But it sounds like the soldiers guarding it are not dying (which would prevent the flag from lowering). Therefore, it seems you have found a bug. Try downloading the patch and hopefully that will clear it up. If not, let me know. Worst case, skip that tutorial and jump right in.
Gal Civ II: You're right that SF did a bad thing. But, it didn't hurt Gal Civ, it helped them tremendously. They got tons and tons of good press for this. SF got tons and tons of really bad press for this. This turned into a huge publicity boon for the makers of Gal Civ.