Firstly, as ever, the eloquent Mr Hancock has expressed my feelings in a wittier, sexier, and (dare I say it) far more hirsute manner that would be possible for me to. Secondly, I'd like to further dispel any notions that you're anything to do with the problems with the game, Mark - as evidence, I present to you the fun we had playing your villainous Forgotten Futures game -mwah, hah, and indeed, hah.
I would echo Jon in laying the blame at two things; the system (Pathfinder) and the interface (Roll 20). The system first - this isn't the first time I have played Pathfinder (well, sort of - the campaign I'm about to talk about was D&D 3E) and we experienced very similar problems there - the encounters were taking a long time and felt very mechanical, with almost no room for innovation or improvisation. At the time I thought it was a problem with my last group (and I include myself in that) but now I'm starting to wonder if it's the system itself. I know a lot of people have issues with Pathfinder, but I'm fond of it as a system and quite familiar with it, so it's a shame that I'm getting highly suspicious that the system just doesn't allow for the kind of 'winging it' that I enjoy so much with roleplaying games. As BigJackBrass has said a number of times before, a system which has a feat for performing special combat maneuvers with a bow and arrow (such as pinning shirts to doorframes etc.) in effect tells all the characters that -don't- have that feat that they can't even attempt it.
The interface - for me, unfortunately, Roll 20 seems very good at bringing my least favourite aspects of RPGing (the number crunching, moving by ruler, combat maneuvers dictated by location) to the fore, and minimising my favourite aspects (the banter, the characters, the plot, the improvisation). By visualising a lot of the game on the board, it has the effect of preventing me from imagining what's going on, and so drawing me out of the game. It's an impressive piece of programming, to be sure, but I feel that it's having a restrictive, rather than a liberating, effect on our group - or, at least, on the parts I like the most (i.e. the roleplaying). As it is, when we try to roleplay, we actually feel like we're slowing the game down rather than adding anything too it.
A third point, I guess, is that because it's a visual interface, it can't really help but make the audio harder to follow and so a little less interesting.
Again, to re-iterate, nothing to do with your GMing, Mark - we've had great (and more concise!) games from you before! As my estimable colleague BJB says, this may come across as too negative, but I'm hoping it hones in on the problems, and shows you that they're not down to you