Yes, this is for Adrift in the Kaleidoscope, trying to get as much input on it as feasible.
And again, quantifying helps me write and be consistent. I don't expect it to be perfect or anything even close, but I want to do it for a variety of reasons.
Why would Caster skew things in D&D's favor? Caster is a freaking Servant and D&D seems like a world in the Age of the Gods. I mean, looking at what they're capable of doing and the comparative feats, Medea actually comes across as an Epic Spellcaster. And by that I mean somewhere around level 40 when the level cap is half that. What she is described as being able to do as well as what she is shown doing line up well with the capabilities of a spellcaster of absolutely ludicrous levels, provided restrictions on some spells, mostly the ones that deal with the True Magics.
I mean, if the beams are (individually) A-rank attacks (and you can accept my logic about the conversion rate for damage between Servant stats and D&D), then that means that she's essentially spamming 6th or 7th level spells. Even if you take into account her being in an area she's prepared beforehand and having a connection to the leylines and use the Spellpower system for D&D, she still does that (which is very high level in the first place) and then casts other spells at the same fucking time. Caster (without being limited by being a Servant with a comparatively crap master) would make pretty much any D&D spellcaster her bitch. Even people like Elminster (The classic uber-mage) would probably get turned into mush.
Aside from the whole 'mundanes have no defense against magic' thing, which D&D doesn't really do, but that's because it's supposed to be balanced while the Nasuverse almost explicitly isn't. It could very well be that only people during the Age of the Gods could 'develop' magic resistance without being spellcasters themselves, but that's a guess. And D&D-verses are distinctly Age-of-the-Gods-y. Alternatively, patching the D&D system so that you don't gain Saves with skill but rather just have them based on your Feats and base stats.
Additionally, psionics really do cover Thaumaturgy with surprising accuracy (Exempting Bounded Fields), provided one remembers that getting above level 10 is an impressive feat, level 15 is probably a top Enforcer or seriously competent Lord, while level 20 is like the Queen of Clocktower. Someone like EMIYA would probably be level 30. Again, the problem is, as you said, the fact that 'normals' have basically zilch resistance to anything magical in the Nasuverse.
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But where do you get the idea that the comparison would skew the relative power levels of the two universes/magic systems? Exempting the UBER-BADASSES like Caster, DAAs or Sorcerers, and LAWLZ-EXCEPTIONS like Shirou, I'm having trouble finding direct combat magic comparable to D&D magic. Given the relative effort they seem to expend, pound for pound, D&D magic seems moderately more powerful in direct combat, if far, far more rigid and limited. Thaumaturgy seems to do Reinforcement massively better than D&D magic however, as well as alchemy, Tracing would make D&D magic its bitch if it was something someone other than Shirou could do, Nasuverse mages also consistently make mystic codes that are either impressive or outright damn terrifying by D&D standards. I don't have a proper list of feats that spellcasters in the Nasuverse perform to compare to though.
Taking into account that D&D of any setting is effectively an Age of the Gods, yes, the average wizard will probably exceed the average Mangus given equal amounts of effort/talent.
While, overall, D&D magic appears to be better, it's not an enormous gap when you remember how unusual levels above 10 or 15 generally are supposed to be. Really, the only reason it comes across as better is that any asswipe with some time and training can learn it and use it competently without having to worry about element/origin/birth.