As you may have already wondered, can iptables-restore handle any kind of scripting? So far, no, it can not and it will most probably never be able to. This is the main flaw in using iptables-restore since you will not be able to do a huge set of things with these files. For example, what if you have a connection that has a dynamically assigned IP address and you want to grab this dynamic IP every-time the computer boots up and then use that value within your scripts? With iptables-restore, this is more or less impossible.
One possibility to get around this is to make a small script which grabs the values you would like to use in the script, then sed the iptables-restore file for specific keywords and replace them with the values collected via the small script. At this point, you could save it to a temporary file, and then use iptables-restore to load the new values. This causes a lot of problems however, and you will be unable to use iptables-save properly since it would probably erase your manually added keywords in the restore script. It is in other words a clumsy solution.
Another solution is to load the iptables-restore scripts first, and then load a specific shell script that inserts more dynamic rules in their proper places. Of course, as you can understand, this is just as clumsy as the first solution. iptables-restore is simply not very well suited for configurations where IP addresses are dynamically assigned to your firewall or where you want different behaviors depending on configuration options and so on.
Another drawback with iptables-restore and iptables-save is that it is not fully functional as of writing this. The problem is simply that not a lot of people use it as of today and hence there is not a lot of people finding bugs, and in turn some matches and targets will simply be inserted badly, which may lead to some strange behaviors that you did not expect. Even though these problems exist, I would highly recommend using these tools which should work extremely well for most rule-sets as long as they do not contain some of the new targets or matches that it does not know how to handle properly.