I hate to say it, but watching the 1st and 2nd seasons again, I'm starting to think Berman had the right idea by changing the music the way he did. As exciting as some of the early themes were, they DO make the show seem awfully corny and dated now.
The quieter, more classical music of the later seasons somehow made the show feel a LOT more sophisticated.
I was thinking exactly the same thing the other day. It could just be familiarity, too. I identify the latter style with Trek, since it was used for most of TNG and all of DS9. It's familiar. S1 and S2, while more interesting, sound a bit more jarring to me.
...for better or worse.