Yeah, it definately was. MST3K had some duds. It wasn't that every single episode was spill your guts funny. But if we were to consider RiffTrax as a sort of series parallel to MST3K as Star Trek:TNG was to Star Trek, then I would say that the overall series of MST3K was a lot funnier in general than RiffTrax. I think it is the switch over from old bad movies to mostly modern big budget films that has taken it down a few notches. Having never been a fan of the intermissions in MSTK3 and the intentionally cheesy sub plots of each episode, I thought RiffTrax would have been an improvment when I first heard about them, but after having watched several (and some are side splitters! Top Gun for instance) I feel that they mostly fall way short of MST3K. The Riff for SWHS however, I feel ranks up there with some of the better MST3K episodes. Sure, it is no "Overdrawn at the Memory Bank", but it is quite good none the less.
The old episodes of MST3K were scripted right? I am pretty sure the RiffTrax are on the fly, which is probably one of the reasons they are not quite as good.