Insufficient information to really say what's the cause of your issues, but in general, what @Giuseppe Larosa mentions about TCP window sizes, and ACKs, are very important when it comes to TCP transfer rate (a few other variable come into play, too). (More on this subject might be found by searching the Internet for BDP [bandwidth delay product] and also LFN [long fat networks], the latter, though, possibly not quite as impactful in your case.)
There are other variables, too, that would impact your transfer rate. For example, interesting is your UDP loss rate. (TCP is much slowed by packet loss, especially if it trigger time outs.) Also interesting is your PPPoE (with its reduced MTU).
With your UDP transfer rate stats, I wondering whether you might need a shaper. It's seems counter intuitive, but by slowing your transmission rate from your router, effect transfer rate might increase.
Regarding lack of information, to start with, what's the physical interface bandwidths at your two sites. Do either of your site's physical Internet connections have a ISP bandwidth cap, in and/or out? What's the usual latency between your two routers?
