I'm always amazed at the number of people who go all the way back to the beginning of Spiderweb's games; I feel like an oldtimer just because I've played all the Avernums, Nethergate, GF 1-5, Avadon, but I never experienced Exile 1-3. At any rate, for what's it is worth from a completely non-optimizing player, I agree with some of what I saw as the OP's reaction, in that while my normal Shaper run was relatively easy, the game does seem to be a bit more difficult than the usual; my Guardian Veteran run was much tougher than the usual for Hard setting for me -- far more having to just completely abandon some areas even when I felt I should have been able to handle them. The inability to hit some enemies due to level (I know, that should have been a hint ...) was a definite adjustment. Strangely, the "challenge area" (other than the final battle) was a walk in the park as a level 19 guardian. By the end, I did find that only acid artilas were really useful to me -- the incredible strength of acid against tough foes meant I just tried to keep them out of harms way and soak up damage with my character.
I did play straight through twice (never done that before), so I must have liked it, but I'm still trying to figure out why it was harder than usual.