With Intelligent maps it focuses on auto-creating connections via its "Connected Entities" but if a device or interface goes does, you will lose the link on your map, which is not useful for locating visual faults. It would be more helpful to be able to manually build your topology, add your connections, and choose which interface to assign to the sides of the link. You can use the "Connect Objects" feature to change what Interface is assigned to that devices side of the connection, but only when it's discovered as a Connected Entity, as opposed to a manually created link, which is unhelpful it will disappear in the event of an issue. It would also make it easier to show a layer-2 device which is fed from a layer-3 device.
Also, links only changes colors when there are errors, discards, or link failure, which is fine if that's what you want to see, but for me, being able to see link capacity as an assigned color would be significantly more beneficial. Essentially what I need is something similar to Network-Weathermaps that is used in Cacti.
