Lionel is not the only company using plastic gears - they work great on many models, and are standard on most HO. The LC, and LC+ line were originally aimed at more casual hobbyists, many of whom run w/o ballasting track, etc. and I have ballasted track. At least once a piece of ballast got into the gears of my PRR RS-3, which is probably why the tooth broke.
In any case, I really LIKE the engine. So I replaced the original (plastic-geared) trucks w/ current-issue metal gear sets including the center gear shaft w/ helical gear. 6802171510 It runs much slower and noisier- maybe because it appears to be a much lower gear ratio. I have not been able to confirm this through Lionel. It's not "bad"- many like slower-running better-pulling locos anyway.
The first LionChief Plus RS-3s sold had plastic gears - built in 2014-16 I believe.
Original RS-3 PRR SKU: 6-38816
Others in same series:
Denver & Rio Grande SKU: 6-38819, Chicago and Northwestern SKU: 6-38778, NYC SKU: 6-38779 Retail $ 329.99
New (2017) Series w/ metal gears and other improvements incl. Blue Tooth and better sound, Retail $ 349.99
Santa Fe SKU: 6-84697, Delaware & Hudson SKU: 6-84696, Peabody Coal SKU: 6-84698, Boston & Maine SKU: 6-84699
NOTE: the LionChief (NOT Plus) 2017 Blue Tooth RS-3's (Retail $ 199.99 and in sets MAY have plastic or metal gears- I have not researched that.