Bonus points to Jangmo-o: in the demo version, not only do they appear in Ten Carat Hill, but they have an entire dedicated Trial there including a Totem Hakamo-o. Then they don't appear in Ten Carat Hill at all in the final game. Honestly, it would be the perfect place to find them early-game - why did that not happen? OTL
Yeah, encounter rates of 5% and below all bug me a lot. If you're doing it because you have too many encounters in an area, remove some encounters entirely and put them somewhere else (side note: Kalos had a huge problem with too many encounters - your regional Pokédex does not need 450 Pokémon unless you really have somewhere to put them and are actually running out of Pokémon to put in a new place), and if you don't have that many Pokémon and just want it to be rare for the sake of being rare... first of all, 10% is as low as you need to go for that, and second, that's really not the best way to make something hard to get.
ALTHOUGH, SPEAKING OF MAKING THINGS HARD TO GET BY OTHER MEANS... has anyone ever actually used a Mareanie for an in-game team? Because wow, I cannot imagine that. It's locked behind optionally fishing to get lucky with a Corsola (which is already not that common) and then waiting for it to call for help and accidentally get a Mareanie. This definitely toes the line between "interesting encounter method that relates to the Pokémon's concept" and "well actually, no, has anyone ever figured this out?" I'm pretty sure everyone who has a Mareanie either got it by looking it up or by accident. What they did wrong was making Mareanie only available this way and still rare with it; I would suggest making it a possible but rare encounter by itself, then way more commonly called by a Corsola so people who know Mareanie well can use a neat trick to get it more readily.
One thing Alola did with encounters that I actually really like is having different encounters for different patches of grass within the same Route. So here's a suggestion if you really want something to be rare: instead of 5%, make it reasonably uncommon (anywhere from 10% to 20%) and then make it only appear in a specific patch of grass, especially one that's hard to reach (blocked by a Trainer or generally out of the way/off the beaten path).
Something I'm considering for my fangame: the first encounter in every area in my game will be guaranteed to be something new to the area (at least until you reach the point where there aren't any entirely new species being introduced, around Gym 7 or so because nobody catches stuff that late). This way, every area stays interesting and you're not bored to death by all of the repeats - TechSkylander, that is a really good point about how many Routes had Pikipek and Yungoos... - and the area always shows you something new it has to offer rather than make you think it doesn't have any, so you're more interested and more likely to look in the grass than spray Repels.