I'll chime in as I've gone through this transition myself.
In my specific case, I started with a back-rack and tonneau cover with the idea of going with an external mounted system for RTT or something similar down the road. To preface all this, I may be a bit of a unique case in the fact of carrying fire gear and other equipment with me (while not traveling) I don't want in my cab but I want to remain dry and secure. This drove a lot of my decisions. For this reason, I moved away from the back-rack and sold it off. I found keeping equipment in the cab didn't work for me, was messy and I prefer as clean a cab as I can maintain.
Enter the cap. Found one on CL for $300, had it painted for $400 to match my truck OEM paint. It had a roof rail/rack system already in place which made for a solid spot to mount to. On top I have a flat grate style metal cover (hard to explain, not what it's designed for - but it works for me).
Mounted to that is a flexible 80w solar panel, emergency LED lightbar, side 'scene or area' lighting, a Smittybilt awning and I have room for traction mats if I want.
Based upon specific needs based on the current 'mission' I can move things around. I used L-track cargo track mounted top and bottom of my side window which accesses the bed area. If I'm running trails frequently, don't need bed access, etc. this works great to leave my traction mat/shovels easily accessible. If I need easy access to the bed (not traveling) I can either leave them off or keep them up top.
I found recently during a trip to Oregon the quick access to the bed area (where I sleep) was nice for transitioning valuables out of the cab to my bed at night. This was mainly a road trip and not as much off-road, so it's more situational to me than anything. The left side of the shell is an integrated plastic bin which I use for electronics of the cap, some fresh water storage, medical supplies, toiletries, basically anything I use multiple times a day and want easy access to.
After all my moving around I found the 'platform' of having a shell to be invaluable to me. I can really move things around and experiment but at the end of the day for my use it works great. Any time I need vertical space to haul furniture or something larger I just borrow a 4x8 trailer from a buddy or family member. My shell rarely leaves the truck at this point.
EDIT: Sorry for all the pictures, found some better and more recent ones that hopefully give you some ideas you can do with a cap.
Side cap storage area for electronics.
View inside bed with right side access window up (handy for dropping camping gear in or accessing the fridge)
Super basic drawer/platform system I built, wouldn't have been able to fit this or keep it dry without a cap.
Top wire grid and solar panel.