I (others...) noticed that the jquery-ui you provide with the core app doesn't include everything that jquery-ui normally includes.

Any particular reason? If developers want to code with that and your included version is missing what is needed, that's an extra (and coliliding load) of jqueryui that could/should be avoided on such a baseline library. Also, the core version provider is legacy now, new version (marked for jquery 1.7) is 1.12.1; IPS included version is 1.11.4

DEFAULT:
 

/*! jQuery UI - v1.11.4 - 2015-03-11
* http://jqueryui.com
* Includes: core.js, widget.js, mouse.js, position.js, accordion.js, autocomplete.js, button.js, 
datepicker.js, dialog.js, draggable.js, droppable.js, effect.js, effect-blind.js, effect-bounce.js, 
effect-clip.js, effect-drop.js, effect-explode.js, effect-fade.js, effect-fold.js, effect-highlight.js, 
effect-puff.js, effect-pulsate.js, effect-scale.js, effect-shake.js, effect-size.js, effect-slide.js, 
effect-transfer.js, menu.js, progressbar.js, resizable.js, selectable.js, selectmenu.js, slider.js, 
sortable.js, spinner.js, tabs.js, tooltip.js
* Copyright 2015 jQuery Foundation and other contributors; Licensed MIT */

IPS VERSION:
 

/*! jQuery UI - v1.11.4 - 2015-12-21
* http://jqueryui.com
* Includes: core.js, widget.js, mouse.js, position.js, draggable.js, droppable.js, 
resizable.js, sortable.js, datepicker.js, progressbar.js
* Copyright jQuery Foundation and other contributors; Licensed MIT */

I understand that there is some duplication with some ips built in js methods however in some (many?) cases the duplication is not the same.

It's just sensible to only include what's needed - makes for a smaller file, less JS to load on every page.

The 1.12 branch removed support for some IE versions which we still support, so we have not upgraded just yet.