Yes it will be slow because frivolous things like scan lines, blur and even a real time rewind feature are on by default, once it's all set I'm getting perfect speeds playing MGS 1+2, Sorry for the delay folks I've had a busy week.
Copy of my config with key bindings for a dual shock 2.
msx key matrixes are really annoying so I hope this helps someone avoid the headache I went through.
located in .openMSX/share/settings.xml
http://pastebin.com/hDYqPah6
If you want the controller to be able to
open and navigate the on screen menu's it requires changing one of the tcl scripts located at
.openMSX/share/scripts/osd_menu.tcl
http://pastebin.com/cnbMP6cj
Look at the function "proc do_menu_open {top_menu}" and "proc menu_last_closed {}" if your inputs are different from mine.
And just for reference the start.tcl I used before I finalized the xml config.
http://pastebin.com/CwfduJt1
If anyone needs help ask away, and I'll do my best.