NAV has a VERY limited number of global dimensions...2.
NAV has difficultiy with companies that may want to track multiple corporations within one NAV "company".
NAV's intercompany (Inbox / Outbox) transaction processing is an absolute joke. Cannot drilldown from the consolidated company.
NAV is messy; window after window opens, and remain open. Horrible design, especially on small-format screens. Every hour (or more often), you need to go through all the open windows and close them, dozens or more.
NAV, despite the apparent root of its name being "navigate' is incredibly hard to navigate, it is hard to find the path to your desired result. If you don't know the precise phrase to search for in the search box, it won't give you what you're looking for. Apparently no intelligent search algorithym. And don't get me started on the inscrutable error messages.
NAV has lost its ability to allow users to customize and produce their own reports (gone away with 2009's Classic Client); off-loading report-building to $$$$$/hr consultants or simplistic Excel worksheets.
NAV cannot deal with non-contiguous data ranges; chart of accounts, and hence, financial statements, need to be in chart of account order. And, also, since 2009, chart of account "numbers" need to be alpha, numeric number series, anywhere within NAV, are not handled well (actually, not handled at all, it's all alpha sorting and range selections).
Data entry speed is not a consideration according to NAV developers. Hands are constantly moving from numeric keypad to alpha area and back, eyes are roving up and down, tabbing across non-entry fields, dropdown lists of 5 selections at a time...
NAV does not allow for wildcard selections in report filters.
NAV is slooooooow. Things (like location codes --- see other posting above) disappear.
There are so many flavors, versions, customizations, of NAV that finding experienced people for your particular installation becomes a situation of just finding someone who can deal with messy software. Customization becomes a crutch for a poorly written and maintained underlying structure. Not to mention, you start to wonder just how many times 'your' customization has been billed out to other customers to deal with still another inadequacy in NAV.