1. "Take away VIP weapon benefits and give them more cosmetic ones" - Even though payments made by players are de jure considered to be donations, it would be inappropriate to abruptly remove those weapons, which are a direct result of their payments, without consulting the VIP community first. However, this is likely rather unfeasible and will not yield any fruit. So, I propose giving all registered players a chainsaw and a sniper as standard weapons for all classes, while leaving features such as car modding and a greater skin choice as VIP-exclusive, and also lowering the price for acquiring the VIP status.
2. "Rearrange all weapon packs and thus balance the battle power of each class, make additional civilian and terrorist classes, turn the civilian class into these: allied - hostile - neutral, downgrade all dual wield weapons (uzi and handgun) to single wield, create a command for the president to make allies from civilian class" - I believe these are rather drastic measures which would fundamentally change the powers/functions of the classes.
3. "Hire more admins and resolve the hacker problems, make all 100% determined hack detections, permanently banned, make cooperation between "clan" players in hostile classes punishable" - New mods are usually selected every 3 months. Also, during the mod selection period, the status of the existing mods (at that time) is closely examined - whether they're fit to be promoted to admins, resume their post or be demoted. This is a very sensitive issue, as it's not just about accumulating a greater number of staff members, it's about who's really able and willing to handle the duties. As for cooperation between members of hostile classes, this is indeed punishable. When such behavior is detected or recorded, those involved are always punished/warned.
4. "Put neutral civilians into godmode without the ability to hurt or be hurt by others
Implement more avatar skins" - I agree with these suggestions. For the first one, as Yomama pointed out, make sure their vehicles are destructible. Regarding the second one - yeah, a couple more skin options for regulars would looks nice and perhaps even motivate them to donate for the chance to select any skin they desire.