skQuery is right out the window. Don't use that for GUIs. I would rather re-write the entirety of skript than use skQuery GUIs.
skript-gui can get the job done, but it will probably break due to a lack of support, and parse times can get pretty slow if you're doing a lot.
Normal Skript GUIs aren't perfect, but they get the job done. and probably won't ever break due to there being actual support for it.
In other words? Use vanilla skript's GUIs.