OK - there is a lot to reply to... so here goes.
I said "You cannot control packets coming INTO your network".
You said "I don't believe this is completely true"
You cannot stop a packet arriving. Therefore if you block it, it must have still arrived. If you keep rejecting these packets, more will come. You cannot control packets coming into your public interface as you have no control over what some other router will send to you. You are right that you can drop or reject and IF the sender chooses to re-send, then yes, of course, the packets will come again. But that is the problem, if you reject, they still come back again!
Therefore if a large amount of packets come into your interface, your interface could become flooded with more packets than your interface speed can handle (or the operating system / CPU can handle). How can you now apply some QoS rule to such an interface that you have no incoming control over?
As you elude, SYN-ACK is for TCP packets. Therefore your suggestion is to respond to it and to reply to possibly ask the other end to re-send. But as you also suggest, this is no good for those protocols not based upon TCP, such as UDP.
So, my original statement still stands. You cannot stop a packet coming into your interface.
You said "Thus, the more tcp traffic is dropped on the incoming interface of the router, the less data remote server will send"
I disagree. if the remote end is attempting to send you data and you drop packets, it will simply keep sending more until they get through to the destination, or until eventually the higher layer system (perhaps some FTP Client) tears down the connection with a timeout. But simply dropping packets or rejecting them, does not in itself stop more packets coming into your edge interface.
Tarpitting is probably better at slowing down the connection as the remote sending end will have to wait for each ACK for a long time, thus slowing down the traffic flow. But it still does not actually "stop" the remote end from sending them to your interface.
Regarding backhaul capacity, you said "IMHO this is not a realistic working modus. This would mean a backhaul running 54Mbps connection rate....." and "Any infrastructure is never big enough to handle all theoratical maximum traffic."
I am not saying that you take all your clients, add up all their theoretical maximum bandwidth speeds, then double that figure for your backhaul capacity figure. You have to look at your actual realtime mean bandwidth levels and if they go over 50% it's time to plan for what to do next as if your mean is running at 50%, your peak will be greater and will potentially affect your QoS. Have look at "Erlang".
You say "Putting too many mangle and Qos on these could actually degrease the performance"
Our CPEs are all 433's or better. They are more than powerful enough to handle the rules we have on them. With plenty of CPU to spare. You do not need many rules anyway. Some simple rules to limit sustained high contention upload speed based on contention-rate, some rules based on protocol to favour one protocol over another. Nothing clever nor too much for the CPU.
Regarding NV2. It has QoS built into the protocol which is why I suggested it may be worth investigating as an option. We have one link running NV2, one AP on the tower and two test clients about 5km away. We are using one HT channel. It is early days, the link has only been running for a week. So far, so good for a link using SIP VOIP and internet data. But, like I said, it is early days and only after a lot of testing will we consider placing the system across all our clients. I have yet to make a lot of phone calls while trying to saturate the link with high levels of data. As they say, one thing at a time. First I am testing the RF environment and interference protection. Next we move to what happens when we move real data over the link.