Yep, the Wartable just feels like an extra thing totally unconnected to the game play. I imagine they had better ideas for it but didn't deliver. Really, the entire Inquisition feels the same. Nothing comes from rebuilding Skyhold, the inquisition's forces are never used or tested. Agents just sit there providing ticks for your perks. All very dull.
I would've gone a totally different way and made it more like a war game:
You take quests by taking missions off the wartable, access to the huge environments is gated by the missions. You can still explore and find things not on the wartable after you "secure" an area.
The inquisition starts with just your party. These are the forces you deploy to complete missions and you do them by turning up in the area and completing the quest.
As your Inquisition grows, you can send out parties (which you control) led by agents or companions + inquisition minions. These might be Templars if you sided with them or mages if you sided with those or just normal inquisition soldiers. The equipment and effectiveness of these minions improve as you perform Inquisition requisitions. For important missions you take a squad of full companions.
Companions and agents can get sidelined as they get hurt and need time to heal, the strength and composition of your inquisition forces changes as they are lost in missions and as you recruit by doing tasks on the wartable. Failure should definitely be an option.
The building options in Skyhold now matter in terms of providing care or better offensive or training capabilities for your forces.
I'd have some special missions where you have to send a squad off that you can't control and trust they'll come back successfully. Some other missions where you have to simultaneously control 2 squads in 2 missions to complete parallel objectives. In the end I'd have a large fight where the state of your inquisition and the quality of your agents mattered (probably an attack on Skyhold).
But that'd be a completely different game.