I like the Neelix gypsy comparison, not one I'd considered. He adapted way too quickly for my liking, again cheated of a good potential character arc and too often played for bad comic relief and as a bad sparing partner for Tuvok. Poorly managed. As for Janeway I think the Thatcher factor sums it up quite well. The Jadzia comparison is interesting, I personally never liked Jadzia that much, I feel she rarely got a good story and apart from the Worf storylines I think she floundered a bit, not surprised that Farrell eventually left the show.
The Trellium addiction stuff was quite a nice idea but I was never quite satisfied with its execution, the allegory of having a recovering addict didn't quite fit a Vulcan IMO. That said it was new territory and certainly a good story direction. The romance stuff was just plain odd, the neural-pressure therapy scenes were more embarrassing than anything and made the whole setup feel a bit of a fanwank to me. I think it was much better handled in the forth season and like you say ended nicely with the Terra Prime ending.
The reading of Data's behaviour is quite difficult. I think Spiner did a great job treading a fine line between showing expression and not being outwardly emotional. Data's empathy, loyalty, friendship, etc, could all be explained as you described as responses to sensory stimuli and could well be something more as we don't understand how consciousness works, I think that ultimately the show was wise to try and keep it ambiguous, not explaining it properly hasn't detracted from Data's character.
With regards to Enterprise, all I can do is shake my head at the fact it was cancelled. There were plenty of not so good episodes and plenty of rehashes as I've already mentioned, but there was plenty of gold in there and it was getting better all the time. I get frustrated with the people who disliked the angry-Vulcan change, the more I think about it the more I come to the conclusion that not only was it a good story thread but it was probably an essential one for the show.