It was good for them to get knocked down a peg. They couldn't simply stay the strongest power forevere just because they could adapt all the time. Having something else come along to blow them out of the water leading to a temporary alliance (Species 8472) was a nice touch. Giving me a nice feeling of Conflict Freespace: The Great War, which I've just completed (after technically 20 years). The ability to level the playing field made all the more sense being in a world full of new races and technology. It was the only Star Trek series which - to me - had an actual point, the first series and Next Generation was "look around and fap", Enterprise was "learn to look about and fap", Deep Space Nine was "Sit there whilst people pop over to fap"*, Voyager was "Look around, fap whilst getting your family home."
*Very vague and probably incorrect assumptions, I've barely (if at all) watched them, except for the first series of Next Generation which I owned but Wil Wheaton put me right off watching any more.