I would be happy if we could, for example, recruit Templars and get those mages that were clearly against Fiona's decision. Or go after mages, but still be able to contact some Templars to join us (those would be most likely the ones outside Therinfal Redoubt). I know some Templars can join us thru war table mission, but it's not the same.
You can kinda sorta pretend around this through the war table missions where you get to shelter mages or Templars who didn't join the rebellion once you get to Skyhold, but like you said, it's not the same. It's a one-off mention and you never hear from them again other than through those war table missions that don't change wording regardless of your recruited faction.
One thing I did think to do on my Knight-Enchanter who conscripted the mages was to built the Templar tower at Skyhold, instead of the mage one, because I wanted to actually see those Templars I was supposedly sheltering - it doesn't have any gameplay effect, but it helped with visual immersion a little bit. (the opposite isn't necessary if you recruit the Templars, I find: you still always end up with plenty of mages walking around Skyhold to keep the visual balance)
I would also love to be able to pick Templars and have Samson as my enemy or the other way around. But that's mostly because of rp reasons.
I will forever lament that the Samson and Calpernia missions are mutually exclusive at all. Both are serious issues the Inquisition should have dealt with either way. How does disarticulating the Red Templars stop being important because you saved some Templars? How does stopping the Venatori from infiltrating Southern Thedas stop being important because you saved some mages? It's weird how you just shrug off this incredibly serious issue on either side and just kind of... leave it to sort itself out.
Plus the fact that through BTD you don't get any of the information on Corypheus you find through UHS makes the endgame feel so... empty. I'm struggling with finishing a mage-siding playthrough right now because I can't shake off the feeling that Corypheus is still just an abstract threat to my Inquisitor. You know nothing about him without the Calpernia quest, you don't understand him or what he's doing at all other than being a generic bad guy, so it feels like my motivation to fight him is just Morrigan telling me we should.
Like, I get what they were trying to do by branching these quests in terms of replayability, but I still can't help feeling the story feels incomplete, whichever way you go, without your Inquisitor going through both.