I actually agree with the premise of the original post and I am the last person that would ever be considered a gusher for VOY.
This episode is not that bad. The warp 10 ceiling was actually established by Gene Roddenberry during the first season production of TNG, despite what Riker says in AGT. You simply have to accept the fact that in the alternate future of AGT Starfleet had redrawn the warp scale again, as happened between TOS and TNG. Just because the scale changed, doesn't mean the speed changed. 32º F isn't any colder or warmer than 0º C. But I digress...
Let's see... Brannon Braga doesn't understand how evolution works and thus the main thrust of the story is just silly. You don't just poof and evolve into something for the hell of it, it's a process of natural selection.
Well, actually you're making a layman's mistake of confusing natural selection with evolution. The two theories are normally linked, but they are not the same thing and in this case natural selection has nothing to do whatsoever with what happened in this episode. I'm not going to go into further explanation of Darwin's theories and subsequent scientists' theories regarding natural selection and evolution because it detracts from the discussion at hand, but suffice it to say, linking the two for the discussion of this episode is inappropriate.
Outside forces dictate evolutionary progress. Might that mean evolving into lizards having sex in the mud? Maybe. But not just because he went really really fast in a ship.
You're on the right track in the beginning here. Yes, external (as do internal) forces do dictate evolution and yes, it is possible that we
may one day evolve into big salamanders but it was never posited in this episode that the reason was because he went really, really fast. What was posited was that Paris attained infinite velocity (i.e., simultaneously occupying every point in the Universe at once) and that this state affected his biology in a matter that caused accelerated evolution. What you're suggesting is that going really, really fast makes humans evolve into lizards (according to the ep.). No. According to the ep. attaining infinite velocity causes a process to begin, not a specific end-result.
Another point regarding evolution and this episode that I never see brought up (except for by me about 6 years ago) is that the reason Paris and Janeway evolved (or de-evolved) into the beings that they did is because the accelerated evolution had a very narrow internal and external template to adapt to. Evolution usually takes place over hundreds of thousands to millions of years. During these eons an organism's internal and external influences are in a constant state of change, therefore it evolves accordingly. Well, in this case, these eons never happened and the internal and external influences never changed but the accelerated evolution responded in the same manner that it would have if they had.
To put it simply, think of a human being living on a starship in a controlled environment with high-end purification systems, synthesized food, 24th century medical care and a basically sterile environment for hundreds of thousands or millions of years with absolutely no change to the environment whatsoever. According to that criteria (due to the accelerated evolution) the salamander may very well have been the end-result of that accelerated evolution.
I personally believe that the big problem that people have with this is that nobody (and I include myself in this group) wants to consider the idea that we could eventually evolve into creatures that were like what we saw in this episode.
The real problems, however, with this episode are the same problems that plagued the entire series as a whole. Mind you, I do like VOY, but what really made this episode go off the deep end of ridiculous could have been easily resolved if the issues weren't so inherent in the series.
1.) The whole concept of this episode should have been played out into a 2 episode story arc. I think this ep. is 41 minutes in length and they're just getting into the story by minute 38 and then they wrap it up wit this ridiculous ending to squeeze the whole story in.
2.) To further that, they abused the reset button again proving that it's not just for time travel episodes.
That being said, I think
Threshold, like a lot of VOY ep.'s had a great deal of potential that was squandered by poor execution.
-Shawn
and right at the end there was a Janeway and Tom scene that was well done. 
