There was a 21-page critique of the series finale floating around the net someplace, but a cursory search didn't turn up anything. Off the top of my head, there was (SPOILERS) Janeway ignoring the temporal time directive, her admiral self deciding to show up then to save the crew rather than, you know, the very first time that Voyager was chasing the Maquee around in the nebula in the Alpha quadrant, the fact that the Admiral gives tech to the Captain rather than the Admiral just doing it with her own ship, the fact that nobody on the ship steps foot on Earth or that the celebration at the end of the series is barely two minutes long... Yeah, there was badass weaponry and all, but there were too many plot holes to make it a practical ending. But that's just me.