transparent proxy => ISP proxy chain

My ISP throttles to a snail pace non-proxy requests.
I have some programs on my computer that dont support proxy.

Can I configure transparent proxy o my mikrotik router and have transparent proxy forward requests to my ISP proxy instead of directly to the web sites ?

Of course you can.
See this Wiki entry.
Under Services → Web Proxy, add your ISPs proxy server.

Cheers
-Chris