I don't have any issue at all with the fuzzy travel time in Trek. I do, however, have major issues with the lack of an understanding of scale.
The galaxy is incredibly, incredibly huge. Within 100 LY of Earth, there's about 10,000 to 15,000 stars. Within 200 light years, there's about 100,000. And yet most "empires" in Trek are shown to have little more than a home planet and a ragtag collection of colonies with a few thousand people on them. Maybe a few remote bases. That's about it.
The logical conclusion from all of this is the Trekverse galaxy is like 99.99% empty, lifeless worlds we never see, and don't even show up on star charts. Or else the Trek galaxies don't resemble the real Milky Way at all, and are much more sparse. Because there should be orders of magnitude more...everything! More ships, more bases, more colonies, etc.