Season 3 of TOS is far and away the worst of the entire franchise. Day of the Dove and All Our Yesterdays are the only episodes I would call good. I think Spectre of the Gun, The Enterprise Incident, Is There No Truth in Beauty?, the Tholian Web, That Which Survives, and Whom Gods Destroy are...okay. Everything else is unmitigated crap.
Season 1 of TNG is the next worse season. However, most of the badness is piled into the first seven episodes. Out of these all of which other than Encounter at Farpoint and Where No One Has Gone Before are embarrassingly terrible. After that, the season is mostly just mediocre, other than the awful Angel One, and the legitimately good The Big Goodbye and 11001001.
TNG's second season is underrated, IMHO. Sure, Shades of Grey and Up the Long Ladder are terrible, as you noted. I'd also put the nonsensical Time Squared in the same boat. But there's a fair number of good episodes as well (Elementary Dear Data, The Schizoid Man, A Matter of Honor, The Measure of a Man, Pen Pals, Q Who?, and the Emissary). The rest is unmemorable filler.