As far the shuttles, I'm thinking there's a few solutions. One, they're cannibalizing parts of the decks that no one is using. Two, they're finding random space junk and Tom, while not in the brig or playing on the holodeck, is creating shuttles out of whatever they find. Three, they've reconfigured the replicators to be continuously spitting out shuttle parts, which why everyone has to eat in the mess whatever mess they're serving.
That has always been my theory. Tom builds the Delta Flyer from Scratch, and when it gets destroyed in one of Janeway's Borg crusades ("Unimatrix Zero") they build the Delta Flyer 2 and test drive it an epi or so later (in "Drive"). So SOMEONE is clearly building shuttles -- I imagine a small team of B'Elanna's engineers hammering away in a cargo bay on a full time basis. I mean, what do those 145+ people do, some of whom we only ever get to see wondering the corridors or hanging out in the mess hall? (Oh, and I think the shuttles Tom wrecks/crashes tend to come back to be fixed -- as in "Once Upon a Time" or "One Small Step". When Chakotay gets hold of them, they are GONE, baby, GONE.)
As for the main thread -- does it get better? There are some really good ones in Seasons 2 and 3, but 5, 6 and 7 have the highest percentage of winners in my book. The one I mentioned above, "One Small Step," ranks among the best hours of Trek -- if you look at it as expounding on the wonders of space exploration.