I dunno... replacing skills is one thing, but right now we're talking about replacing in-game items that you used to be able to purchase with gold coin. So far there seem to be at least 3 inventory capacity perks and 1 potion capacity upgrade. These don't seem like things you can easily skip. I remember having a heck of a hard time dealing with inventory in DAO until I bought the final backpack (and they were spread out and hidden all over the place). If health regeneration is eliminated in DAI, then potions well be invaluable on all but the lowest difficulty settings.
I think it would be best if we can unlock most, if not all of these perks eventually... perks like "additional codex exp" can be substituted by killing more enemies, but backpack and potion upgrades are almost mandatory. I'm not totally against limitations, mind you. I am simply having a hard time imagining myself ever passing on those 4 perks, no matter what type of Inquisition I'm trying to created (diplomatic, militaristic, etc...). Some of the perks don't really seem optional, you know?
The backpacks were really important in DAO because of the lack of storage(basically making Warden's Keep "required" DLC). In 2, they were less important because you get access to the storage before you can hit the inventory limit. Sure it'll be nice to hold more items, but if Inquisition is like Origins and 2, those bodies holding loot will still be there until the point of no return resets them, so you can get back to them if you reach the inventory cap.
As for potion limits, it's unclear as to what that entails. It could mean you can only hold X health potions. It could also mean you can only hold X different potions. Without further information on the subject, it's impossible to make a determination on it's necessity(though I agree that I don't see myself passing on either on a first playthrough unless i'm forced to).
All that said, putting a limit on the number of Inquisition perks would be no different from limiting abilities/skills in Origins. Yes, I can see that some perks will be taken all the time because they are extraordinarily valuable in comparison to others, and not taking them would be a form of self-imposed difficulty. But that's no different from Origins. After all, Mana Clash is all but mandatory on higher difficulties, and very few take a pass on Master combat tactics and Coercion for the PC unless they are doing it on purpose...