Would a Fugitive Scientist squaring off against lots of people without investigation win at a story that was Parallel Universed?

He would win all the stuggles and succeed at the story.

That's how we played it, but the new FAQ says that the non-Syndicate player's skill ONLY does not count for determining the skill STRUGGLE, and does not change the value of the card. Parallel Universe suggests that you simply count all the cards printed skill, not the enact a skill struggle, to me at least

First of all, some references for what we're comparing.

The latest FAQ:
(v1.0) Counting Skill
Some effects reference counting skill or not counting skill. These effects do not change the actual numbers on the card. They only mean that the skill is not counted during the skill comparison at the story.

Fugitive Scientist:
Characters without an Investigation icon committed to the same story as Fugitive Scientist do not count their skill.

Parallel Universe:
When resolving struggles at attached story, count the total skill of all participating characters instead of the icons to determine the winner of each struggle.

My interpretation for how an interaction of those effects goes down:

Normally there's one skill comparison per story, which takes place at the very end of the story resolution to determine who succeeds at the story.

Parallel Universe creates one extra skill comparison per icon struggle, replacing the icon comparisons that take place to resolve those icon struggles.

So, for whatever reason, a game effect or a card effect causes the game to make a skill comparison between two players at a story. The game gets a head count of all the committed characters controlled by each player at the story and then "counts" them one at a time -- by targeting them, much like many card effects must "choose" something to see if it's a valid target before resolving that effect.

A character who skill "is not counted" cannot be targeted by the game "counting" it for a skill comparison. The character doesn't report a 0 back -- it doesn't report back at all. Subsequently, that character doesn't contribute to the skill comparison in question.

So, if a Parallel Universe story is being resolved with just a Fugitive Scientist on your side and any number of characters without investigation on your opponent's side, the Fugitive Scientist is the only one ever successfully counted in the skill comparisons, and thus you win every icon struggle and succeed at the story, both uncontested.

That's how I see it, anyway