The changes to the names didn't bother me so much, except that it showed an utter lack of creativity. Instead of creatively inventing a logical predecessor to the tools who know in modern Trek, they just changed all the names to something that sounded more primitive when they all functioned the same.
That alone really wasn't the problem, but just a symptom of it. That lack of creativity really did show itself in the quality of the characters and the episode writing as well. It just seemed that Berman and Braga were cranking out episodes focused more on quantity than quality, especially during the first two seasons. All these things started to improve in seasons 3 and 4 when B&B backed off for the most part(alas not in the finale), but by then the damage really was done.
The characters just lack when you compare them to their counterparts in the other shows, and in the end, one good season, one average seasons and two crummy ones with a few standouts, just weren't enough especially when the damage was done in the first two.