Let's go over the main thrust of the question:
However, I'm aware that the there are some episodes, in the first two seasons especially, that are...less than stellar.
Given the nature of the show, I'd like to skip or avoid these episodes whenever possible. Ideally with the following in mind:
- Any episode that gets referenced later, in this series or in ones to come after, I do not want to miss.
- Anything involving an ongoing plot, like the Borg invasion, I want to make sure I see.
- Any Ferengi episode I do not want to miss, because I'm especially curious about their 'evolution' in Star Trek.
But as for the rest of the series, which episodes can be safely ignored, and are most infamous among Trek fans?
Most of this is pretty good. You're looking for S1 and S2 episodes that are later referenced. You want on-going arcs included. You want Ferengi episodes included. These are all clearly-stated criteria, some with reasons for why you want them.
However, the last clause (which you recently edited) is a bit problematic, as it gets into subjective territory. There are some truly heinous episodes, like Shades of Grey, as mentioned in an answer. But most episodes are going to have mixed reactions within fandom, and without some objective measure it's hard to nail down generally well-received vs generally derided. I think removing that last bit will improve things, you'll already be getting a relatively lean list from your bullet points. I recommend you build on that by looking for reviews or recaps of those episodes to see if some are awful.