Classes for alignment should be added to a core CSS file and the buttons should restored to the CKEditor interface. The prevalence of content and the likelyhood of these classes being used makes them candidates for addition to every page of the site. This could be done in a new CSS file, or as part of system.base.css, which includes similar global styling.
Most of the relevant code was removed from the original CKEditor module patch in this comment. This code should be restored as a new patch.
There is an existing argument about whether these buttons should be restored at all. Two camps largely discussing it on two opposing primary points:
In Favor) WYSIWYGs are an end-user feature and we should provide users with the tools they expect from an editorial experience. The use of classes for alignment and underline provide flexibility and consistency for editors, site-builders, and themers. And if desired they can be disabled by site-builders. The alignment buttons are also needed for alignment of images and captions, providing them is a convenience that should allow any item to be aligned.
Opposed) Alignment is layout manipulation that should not be part of content creation. Adopting classes for alignment and underline means a long-term commitment to these classes in our content. This problem should be left to the contributed module space. Underlining does not have semantical meaning (it has to be imitated with a span and an underline class), so it should not be provided at all.
User interface changes
The buttons for left/center/right alignment and underline are restored as available buttons in the CKEditor administrative interface.
None significant. Classes for alignment and underline would become available for styling by themes.
Original report by Wim Leers
Follow-up for #1890502: WYSIWYG: Add CKEditor module to core.
See #1890502-105: WYSIWYG: Add CKEditor module to core.1, #1890502-108: WYSIWYG: Add CKEditor module to core, #1890502-109: WYSIWYG: Add CKEditor module to core, #1890502-110: WYSIWYG: Add CKEditor module to core and #1890502-114: WYSIWYG: Add CKEditor module to core.