Honestly, Season Three, in effect, is the season of "learning to love the Delta Quadrant." At this point, with the Kazon jettisoned and the crew unified from its divided origins (because by this point, the Starfleet-Maquis division doesn't really matter anymore), the characters are able to start getting comfortable in everything they're doing. You can see the characters start to expand their skills and abilities, stories are more about the wonders of this unexplored region of space... The biggest flaw is that, without Michael Piller's efforts, Voyager's crew not just doesn't really expand, it even contracts to just the credits cast - as Season Two went on, he'd attempted to build up recurring characters, the most successful of them being Ensign Hogan... who was a casualty of Basics with Suder and Seska, and Ensign Wildman functionally vanished into the ether until next season introduced Naomi as more than "the baby." The only recurring character introduced was Vorik, and he was played by Jeri Taylor's son.
Season Three is probably Voyager spreading its wings the most, trying to be something special and unique.
The problem of Scorpion, as the finale/opener for next season, though, is the fact that it introduces a show-defining moment for everything. Scorpion makes a pointed question - "what is our mission statement?" Because they have insurmountable odds in their journey forward, so the question the characters, and the writing, face is what is the most important thing for these characters, exploring the Delta Quadrant or going home?
In reaching that point, narratively asking that question, it gives a mission statement. And the one that was chosen was making the point getting home, rather than, ironically, given the way that the series finale tries to claim, the journey itself. The destination was what mattered, not the way there. Voyager's focus was on proceeding forward.
This ended up tying their hands in the way that it cut off so much of the setting - Voyager would always be moving on. Unlike the first two seasons, they would no longer be in an area of space long enough to start having regular allies or enemies - at most, we'd get new antagonist races each season, but nothing lasting. There would be no major enemy, other than the Borg, and that would be a case of diminishing returns, combined with reducing the Queen to a Saturday morning cartoon villain, sitting on her throne and shaking her fist, going "I'll get you next time, Janeway, and your little ensign, too!"
In taking the choice to focus on going home, rather than exploring the Delta Quadrant, Voyager had a mission statement that was in many ways opposed to the ideas that it was built on, built to explore. That's not a flaw of Season Three - if anything, Season Three is a sign of what the show could have been. You hit Season Four and on, and you reach a point where, fundamentally, almost any episode could be swapped with one another in any of those four seasons, and you are not fundamentally upsetting anything - in a lot of ways, you probably wouldn't even need to change the script in any way, aside from the stardates.
It's not the season's fault, though. If anything, it's ultimately the flaw of the people setting the course for the series proper.