I\'m implementing a protocol over serial ports on Linux. The protocol is based on a request answer scheme so the throughput is limited by the time it takes to send a packet
At those line speeds you should not be seeing latencies that large, regardless of how you check for readiness.
You need to make sure the serial port is in raw mode (so you do "noncanonical reads") and that VMIN and VTIME are set correctly. You want to make sure that VTIME is zero so that an inter-character timer never kicks in. I would probably start with setting VMIN to 1 and tune from there.
The syscall overhead is nothing compared to the time on the wire, so select() vs. poll(), etc. is unlikely to make a difference.