Are the packages very large, like Firmware Updates? Are the devices running Android Nougat by any chance? 

Have you tried connecting these devices to a faster internet connection? From Wifi to Mobile Data or vice versa

Does the problem only affect offline devices which are coming online and then trying to install the new packages?

I have also noticed this with about 50 Android devices connecting to a single AP with relatively poor signal strength on the same LAN as SOTI. 50 devices pulling a 50MB package each took about 3 hours to finish. In the future, I may create virtual groups of about 5 to 10 devices max and only deploy large package updates to each group at a time until all are applied. You could also test a self serve profile on a single device to see if that mitigates your issue.

Is the MobiControl server local to the network that the devices are on or is it a cloud environment?

Hi Fredrich,  I assume you have already checked and it's not network (poor wireless signal, excessive collision, etc ) or insufficient bandwidth (for big chunk of data)  issues.   if you experience "general" profile deployment delay for hours/days (i.e. not just for package version change within a profile, but also for any other payload change within profile),  you might need to check if you have enabled any firewall on your deployment (DS) or management (MS) servers.  If so, make sure port 5495 is enabled in your firewall(s), even if both DS and MS are installed on the same MS-Windows physical/VM instance.   Packets from DS module might go out to your firewall and get routed back to your MS module on the same server instance via port 5495.   When such inter DS-MS data get filtered by the firewall, your updated profile deployment will get stuck and delayed for hours/days.  With port 5495 traffic unblocked, profile deployment delay should be gone right away.

One simple test to see if blocked 5495 port is the problem is to shutdown and restart your DS+MS.  If pending profiles/packages get deployed to all on-line devices right away in reasonable time, but another change to your profile/package get stuck/delayed again.  Then, you can start checking your local or external firewall rules blocking port 5495.