You mean the lack of science in the science fiction? Yes, that irks me to no end. The type of thing you're talking about is that smart writing that Trek is known for, which is sadly missing from the more action oriented reboots. They're trying to substitute clever writing with action and special effects, which works in other films but isn't the best recipe for Star Trek.
Originally, Star Trek got by on its writing. And, that writing was done with the help of real world scientists acting as technical advisors (which many were happy to do) to make the future science as realistic as possible. Here's hoping the new series brings back these elements.
As for alienating new viewers or not, it depends on the viewer. Some will love the new formula, others not so much.
such as the heisenberg compensators in the transporter system. it's always amazing how much technology from the show has inspired real life technology (flip mobile phones, ipads, google glass etc).
i think i remember reading something somewhere a few years ago (maybe before the 2009 reboot, which I shall henc forth start referring to as STR) that the studio wanted to get away from the Trek-speak as they felt it cheesy and that it was off-putting to a wider viewing audience. Personally I think it's a mistake to reject part of the identity of the franchise that it became famous for. It's almost the same as Disney deciding to remove the force from Star Wars as it's too spiritual and may be off-putting to a wider viewing audience.
