Captain Puckett felt strongly that the plan to ditch the rail engines in favor of tugs was one that they were going to regret. Furthermore, if the tugs don't work as he predicts there will be NO infrastructure to install the rails. As a result the Panamanians will need to go back to the drawing board and re-engineer the locks. Neither a easy or cheap solution.
Essentially the rail engines keep the ship centered in the locks. Having the tugs do this job when the are not anchored and they are subject to the same ebb and flow that the ships are means that they will have a difficult time keeping the ship under control while entering and exiting the locks.
Now, from what I personnally saw, there was still a huge amount of digging and construction that needed to be done. It seemed to me that the scope of the unfinished work was such that finishing in a reasonable amount of time was doubtful.
I haven't even broached the subject of the experimental water saving plan that they have planned. I'm assuming that better minds than mine have determined that it will work. But it seemed overly complicated and very much like a perpetual motion machine.