Part of the problem is that the world is tipping on its side, and it's happening faster each year. Doesn't bode well for those southern vacation spots in a hundred years or so! ;-)
The reality is that in the US we're not updating the VOR MagVars that often, part it is due to the ongoing decommissioning process in the US called the VOR Minimum Operational Network. Adjusting for MagVar requires changes to the actual VOR and the FAA is just behind the problem as they work through the VOR MON program.
Here's an FAA Aeronautical Charting Meeting agenda item discussing the MagVar discrepancies that can happen between conventional procedures and the MagVar in the FMS: Hist_11-01-296 (faa.gov). Here's one on use of MagVar on DMEs: 14-02-284-ACF_DME_Facilities.pdf (faa.gov)
This InFO explains the differences between conventional procedures and FMS tracks: InFO 12009, Magnetic Variation Differences Between Ground-Based Navigational Aid (NAVAID) (faa.gov)
Much of the issues are involved outdated MagVar tables in the IRU, collected by the field and used in procedure development and documentation along with the procedure not being updated. There's been much talk in in various industry groups, including the Aeronautical Charting Meeting, which is going on as I type, about moving towards using the Airport Reference Point as the source MagVar for all instrument procedures tied to that airport.
All of these issues go away if move to True. Magnetic track, course, and heading is presented solely for pilot convenience. The FMs and IRU computes everything in True, then converts it to Magnetic so it agrees with the magnetic compass. Going to True would mean no more runway repainting due to runway number changes resulting from MagVar changes. It would mean no more mis-match between procedure tracks as MagVar changes.
Rich