I feel a lot of complaints come from people who didn't play the games, or went into them expecting to hate them and adamantly stick to their opinions no matter what. A lot of things I notice are especially hypocritical: I've seen people curse gen 5's experience system but praise its return in gen 7, mock Litwick for being an "inanimate object" but fawn over Dhelmise, claim Purrloin is a "copy of Meowth" simply because it's a cat and therefore "lacks creativity" but adore the Skitty line, insult the massive undertaking of fully-animated sprites for "looking weird" (which I can't agree with) but take no issue to the low-quality jpeg-esque textures of Sun and Moon, laugh at the name choice of Black and White but defend any of the other arbitrary title choices despite gen 5's actually tying into the actual story. It's one thing to have preferences, but the sheer amount of vitriol gen 5 receives while its contemporary counterparts get away with much worse issues just reeks of hypocrisy born of some form of ignorance.
I feel gen 5 was just too ahead of its time. Released during a period where most of the people who started with gens 1 or 2 were reaching high school, people were just clamoring for any reason to hate it. Those exact people were entering or continuing "edgy" or "hipster"-like "phases," but with greater capacity to form more (what they believe to be) in-depth opinions than when they went through these motions in middle school. Gen 4 received this kind of backlash as well, but since it's next in line to be remade (and is, as such, getting quite old) people are beginning to look at it with fond, nostalgic memories now. And I believe gen 5 will have its turn one day.
The key difference seems to be that gen 5 just never went through the "recency bias" phase newer games have the luxury of receiving. The general "timeline" for game releases seems to be that the newest games have an overly-positive pre-release and release period timeframe, but the fanbase begins realizing the negatives some months after the new-game hype has died down. Once they get old enough, the opinions that will rise back to the top of the melting pot of thoughts will be warm, joyful, sprinkled with a hint of nostalgia. Gen 5 especially but even gen 4 seemed to have had their first two stages swapped, likely due to the reason I've stated above: the playerbase that was most likely to be using Internet discussion communities at the time was at the prime age to hate or dismiss without reason while still lavishing in their "genwunner" mindset.
Another thing to consider is that YouTube was quite different back then as well. There were no conspiracy theory analysis channels to generate artificial hype, or to discuss the latest rumor posted by some rude jerk on 4chan, and there definitely weren't any official trailers to hype fans by showing the newest Pokémon in action. All we had were blurry CoroCoro scans and text-only discussion boards--a lot of details went by unnoticed unless you followed them all, unlike today where just keeping up with GameXplain is usually enough to paint you the full picture. And admittedly, if you see other people hyped, it tends to rub off on you, which is another advantage the newer games have that the older games did not.
But tldr, I have to agree with OP. A lot of the hate for gen 5 is really at odds with what people tend to like about other (and especially the newer) games, leading me to believe a lot of the hate is just from people who didn't play the games, or from those who did but just "skim played" without actually trying to see or understand what the games had to offer. I'll end it off with a summary of a discussion I had with someone once, not long ago: apparently, the USUM remix of Maxie and Archie's battle theme is good because it sounds fine in the context of their fight, having just proven victorious in their home worlds and trying to push further now into Alola. Compare this to the Alder battle theme in BW, which is bad because it sounds more like a post-game boss battle theme rather than the final battle theme. Yes, the post-game boss's theme sounds bad because it sounds like a post-game boss theme. You heard it here first, folks!