Right, that pilot jet will fatten up the mid range without any effect below 30% throttle and negligible effect at WOT although it does still flow at WOT it's not a huge amount like what comes from the high speed venturi. Everything else needs to be correct first before increasing the pilot though, b/c just a small amount of blockage in those "bypass ports" will cause a lean bog, along with too high of pop-off, etc.
You can try opening up the idle mixture screws to add more fuel but at the potential expense of making the idle too rich. The pilots don't control idle mixture, so going up one size on the pilots won't have any effect on the idle screw position. It's a better design on the top end IMO, with the high speed mix screw, the screw is supplementary to the high speed jet so in that case you can compensate by opening the screw if the high speed jet is a bit too small. I think Mikuni needed a way to get an emulsion to the the idle port, so the natural solution was to feed the idle circuit through the pilot circuit (A really cool idea as opposed to a separate air feed, but I think this causes confusion).
So anyway, it's not a good idea just to blindly increase pilot size without confirming all the other parameters first, could just be gum in one of the "bypass holes" causing a mid-range bog. The carbs have to come off and apart in order to confirm everything anyway, so starting from scratch they have to come off at least twice before I'd break down and increase pilot size unless someone before me had documented their experience. Your ski isn't my boat, different carbs and engine, so all I can tell ya is what I found in my case which may or may not apply.