Personally, I think it was best to leave it on the cutting room floor as it didn't have a proper set-up in earlier movies. Had Quigon actually disappeared or had there been some actual discussion of it earlier in the prequels, it could have been done right.

As it is now, there is a strange attempt to have Quigon yell "Noooooooooo!!!!" in AOTC, but it doesn't sound like him (for obvious reasons) so when he appears to Yoda in ROTS, it seems rushed. I think the reason it was cut was movie was too long anyway, but had George set it up more earlier, he might have had to keep it in.