Point taken; I should have said it was an introductory scenario for the Second World setting but runnable with d20 Modern.
Some of the differences stem from the fact that players in this sort of game can either come from a fantasy background or from the modern background and that gamemasters might actually want to start with a regular looking fantasy campaign then reveal the modern world part-way through. To allow for all the different ways people might use the material the book and scenario includes classes from the PHB and d20 Modern plus rules for how to keep them fairly balanced against each other.
Also, since gamemasters will sometimes run modern day adventures and sometimes pull out a scenario from their battery of fantasy modules you need to at least have a method of dealing with things like alignment since some powers and spells rely on that. One method is to simply dump alignment and those spells, or you could include alignment everywhere, or you could have alignments on the fantasy side but not on the modern side; the last option helps paint the fantasy world as more black & white while the modern one feels more relativist.
I prefer the modern versions of skills too; they're more condense and many have better defined the abilities they give. Craft (mechanical) doesn't strike was as the skill for making armor though. The Second World Sourcebook adds Craft (smithing) as a combined blacksmith, weaponsmith, armorer skill but I left that out of the scenario because I didn't think it necessary.
I thought that most of the feats in the scenario were the ones that just boosted a skill or two and so their effects were already rolled into the characters. I'll post a page with any missing bits. I also figured that since the influence rules were already available as a free download that they didn't need to be included in the module too.
Ease of use and portability is really important to me; I tried to make it so gamemasters could run the module for a d20 modern game without having to write down any new information in the scenario. I take it that part didn't work?
Hopefully, those using a primarily fantasy game could simply ignore stuff like action points and MDT (if they want; they make excellent optional rules) and take the armor classes as given, not worrying about precisely how they came about. That's the way I run modern scenarios in my fantasy games or fantasy scenarios in my modern games. In some cases portability is easy, such as MDT and action points. In other cases portability requires work, such as allowing both PHB classes and d20 Modern classes in the same game; that's mainly because of the Defense bonus decision. There's a large section of the Second World Sourcebook devoted just to this issue and how to make different worlds or planes play out differently by changing the rules used by the different places.
The scenario should work best with an Urban Arcana style campaign where you actually wanted to allow transit back and forth between the modern world and the fantasy one. It'll work less well with an X-files or Shadowchasers style game.
Sorry about the shaky advertising and that you didn't like the module. I felt blending the core rules and d20 Modern material required some of the elements in the scenario. It's made even more tricky by the fact that people's opinions vary widely on subjects like non-lethal vs. subdual damage and wealth bonus vs. plain old cash. Even with spells I have to weather the dice-throwing of my players if I tell them that 8 hour long Bull's Strength doesn't exist anymore but now you get a flat +5 bonus for 8 minutes.