I completely agree with you, they had the wrong sort of geek in season one and I think they spotted it and were given the perfect opportunity with the shifting timelines to fix it for good. Which, if it's true, seems to be proof that we will probably never actually get back to the timeline/universe the show started it.

If does Cutter disappear I suspect they'll bring in another expert rather than adjust Connor any more.

And like you I really want Abby to get the chance to use some of her animal skills. She knows living animals and their instincts far better than Cutter ever should.