Two questions, will character skill levels (specifically those dealing with fleet tactics and maybe industry for salvage) increase the effectiveness of these options?
When reputation is implemented as well, will that have an affect? I'd love to have enemies cower in fear even though they're stronger 
Two answers: maybe and maybe

(That is to say, not something I'm prepared to discuss in detail.)
Finally - and I know this is not a plausible scenario - I'd love it if you, Alex, were to teach the big gaming studios on how game design is supposed to be done, because you'd have a lot to teach them, I think.
Much as I appreciate the compliment, I wouldn't call myself an expert game designer, and I definitely don't want to put down the folks working in AAA game studios. They have an entirely different set of challenges, and I'm sure there are plenty of extremely bright people working there. There absolutely *have* to be, to make something as complex as a big-budget title come together! As with indie games, there are successes and failures. The difference is, we get to hear about the AAA failures and dissect them in great detail.
is logic implemented as plugin (default event handler) or will be hardcoded?
That dialog is implemented as an InteractionDialogPlugin. All the logic is at the moment moddable, except for some AI decisions about what to do (which could also be modded by putting it in the dialog rather than calling into the AI to get its choices).
In a military context, "harass" and "harry" are near-perfect synonyms. As is so often the case in English, one comes from French (harass) and one from German (harry—it has the same etymological root as "Heer," actually).
—your local English major/copy editor/etymology nerd
Speaking of nerding out on etymology, my favorite site ever:
http://www.etymonline.com/I'd be 50/50 on "Change it so people don't need to reference a dictionary" vs. "Hey, you get to learn a new word! How cool is that?"
That sums up how I feel about it. Personally, I
love when games teach me something new. But, I suppose there's a fine line here, between "making something iscrutable" vs "dumbing it down".
I've also got some vague ideas about encounter options (perhaps unlocked by skills) that would allow a smaller fleet to isolate a portion of a larger one to fight against. It's not something I want to start out with, though, but something I'm going to keep in mind in case the campaign shapes up in a way that makes adding something like that desirable.
That sounds like fun, and like it would be a great gift for players who plan to run with small fleets. If you connect it to the leadership aptitude those options could also make the aptitude interesting again for those players. At the moment you have practically only two aptitudes with a small fleet play-stile.
I imagine it would be especially thrilling if you have a timer running down, after which the main fleet joins the battle.
Right! I was also thinking it could be an interesting means of checking the player's fleet size if it was used against them. It could also make smaller fleets suddenly become a threat regardless of how huge your fleet is. This is all handwavy musings about a potential future, though

Also: Ohhh, new screen borders (look at the picture in the blogpost). Supplied by TRIPAD? 
A wholly-owned subsidiary of the Tri-Tachyon Corporation.