When SharePoint 2013 came out, one of the most promising features was the Managed Navigation. Configuring
Managed Navigation in SharePoint 2013 is straightforward and provides great
no-code solution. In this blog,
I will walk through some of the major limitations and why you must avoid this
solution.
 
1) For each site collection you need separate Term Set.
It
 is important to note that each term set can be associated with only one
 site collection at given time. In other words, it requires dedicated 
copy of term set for each site collection navigation. E.g. If you have 5
 site collections, you must have 5 copies of same term set to use for 5 
site collections navigation data.
If 
term set is already configured to use for Site Collection navigation and
 if you try to reuse same term set in another site collection, 
SharePoint will throw following warning “The selected term set is 
already used by another site” 
2) Managed Navigation can’t be secured or targeted to specific group.
 One
 of the great abilities of Structured Navigation was you can configure 
audience targeting or secure each menu item for specific audiences or 
SharePoint security groups. Unfortunately Managed Navigation can’t be 
secured or targeted to specific security group.
3) Manual Maintenance is still required to update global navigation menu items.
 As
 we discussed earlier, you must have 1 term set for each site 
collection. If you have more than 1 site collection, you must have more 
than 1 term set dedicated to each site collection. To ensure, all the 
site collection uses same navigation menu items, there are two options 
available in SharePoint 2013 for replicating term sets. Regardless of 
which approach you may take, it will require manual maintenance of 
reconfiguring term sets when you have changes in term set.
4) Managed Navigation doesn’t apply to Sub Sites automatically.
 This
 is another one of those mind-boggling limitations of Managed 
Navigation. If you have enabled Managed Navigation at the site 
collection and while creating sub sites, if you are planning to inherit 
parent navigation, Managed Navigation doesn’t apply to sub sites 
automatically. To resolve this peculiar issue, you must open Navigation 
page from sub site settings page and click “OK” for to take in effect.
    
5) Managed Navigation doesn’t provide open link in new tab. 
Structural
 navigation provide you check box option to open link in new tab. This 
functionality is not provided in Managed navigation. Though you can 
overcome this issue with JavaScript patch, you need to put this patch in
 master page of each site collection to work.
6) Managed Navigation conflict with SharePoint js. 
Managed
 navigation stops working if you explicitly load sp.core.js in your 
page. The sub level navigation stops populating. I don’t know the 
strange behavior of it as sp.core.js is SharePoint own js file. 
7) Managed Navigation displays additional home tab.  
This is not though limitation but its annoying for sure. Managed
 navigation displays first tab with site name additionally. You can't directly change it or hide it. The thing we need to do with it is mostly hide it with javascript and the bad thing is we need to put that in each and every masterpage.