Recently bought the Surface Pro 128GB.
christ almost a year since you posted this and there doesnt seem to be any solution yet. im in the same boat as yourself, 128GB Surface Pro. windows 8.1 everything updated.
im using a Lenovo bluetooth keyboard and any time there is something downloading or if a program like evernote is syncing data the trackpoint/mouse pointer starts to lag really bad. the keyboard part doesnt seem to lag as much or maybe i just dont notice it.
ive only had it a week and already its getting really annoying switching to the pen just to get things done on it, or having to use the touchscreen if i dont have my pen with me. im hoping it wont take them another year to fix this problem