Pilot's voice seems off. I guess after two years he forgot how to do it the same way.
I noticed this too. Some other differences I noticed-
The pilot's chamber set was different (maybe lost after the series ended).
The Scorpius makeup was significantly different, particularly the skin tone which at times appeared to be nearly white as compared to the beige/gray of the series. (series
The Rygel puppet was different (this was an improvement).
Also if you watch the miniseries immediately after the end of the series like I did both times the change in appearance of some of the cast is a little jarring. Ben Browder got thin. Thin!
I just finished my second watch through about a month ago and I still love this series. It seems wildly original to me and I wish there was more of it. The first half of season 4 is farbot though ... I still can't place whats quite wrong there, I thought it was the splitting up of the characters but there's something else going on. Maybe just too many wacky type storylines in a row.