It seems to be a stigma. 1 point of lethality does less armor shredding than 1 point of flat armor pen used to do. However Riot added more of it to items and runes. If you didn't know, lethality scales with the enemy's level, the way Riot set it up, lethality is weaker than flat armor pen was until level 8. After level 8 it is better, but before 8, it is slightly weaker. I think people just don't like it because of how they usually build it for early game, and now its slightly weaker in the early game. For instance I have seen a lot of complaints about it focusing on how 1 point of each is not equal in the slightest, yet they don't even bother to account for the fact that there's more lethality.
However, by no means would I say it is not worth building or putting on a rune page. It can still give you that early game edge you need, and now gives you less of a diminishing edge late game. I have them on my rune page because back when it was armor pen I found it made a huge difference on my jungle clear times. Since it changed to lethality I haven't noticed a lowering in my jungle performance, so I don't think its that noticeable of a change early game at least(although maybe it is for assassins).
