While generally I dislike silent protagonists, occassionally they are used effectively. Super Mario RPG is a great example where while Mario never really said anything, he pantomimes everything though, and it's carried out perfectly, like when he explains to the Chancellor what happened when he went to rescue the princess. Granted you can't really use that tactic very much in other games, but it was a great exception tot he rule.
I hate the "Load Bearing Boss" trope where somehow a boss's health is inexplicably tied to structural integrity and beating him immediately makes the structure he's in begin to collapse. Cue escape scene.
I hate when games with alignment choices you either have to select the alignment ahead of time or are only given black or white choices. Where's my 50 shades of grey morality?
"Money Spider" Really? Is it so hard to just drop some venom or a carapace that I can then SELL for gold? It makes much more sense and lets you implement other cool features like FF:XII's bazaar system
Thriving Ghost Towns: I hate how the BIG cities in most classic JRPGs are about as big as a SMALL village in reality, I understand the reasoning behind it in a sense, but it still kinda kills me finding 4-6 house villages all over the place that... half of which are shops? That doesn't make any sense! I much prefer when games allude to the fact that "there's more to the town than just what you see on this map, but only this part is relevant to what you're doing.
A few tropes I REALLY like:
All in a row: Where you see all the party members trailing behind you. I hate it in some games where your party members somehow just dissolve into your flesh until the next battle or cutscene.
Kleptomaniac Hero: I hate when there's barrels, crates, dressers, bags, etc. that are just "scenery porn", if I can't loot at least some of them I feel like it's a waste of an easy way to add immersion. I want to be able to take everything I see (not without consequence of course)
Law of Cartographical Elegance: I prefer world maps that do "loop" but if you have the whole world shown want to be able to see an entire landmass not go over the edge
Metal Slime: A hard to kill but extremely rewarding monster
Romance Sidequest: I prefer romance in a game to be optional, but well crafted. I think it really makes it more interesting if you're doing things FOR your party members, not just WITH them.
Take Your Time: As much as some people hate the lack of urgency, I prefer this trope as it allows you to fully enjoy the game at your pace. I tend to avoid standard "save the world" plots to avoid the sense of urgency being at odds with you... say... I don't know... spending 3 weeks gambling.
Turn-based Battles: Preference really but when the rest of the game lacks urgency or action, I don't want my battle system to have it either, I prefer true difficulty in the encounters, not artificial difficulty in timers.
Zip Mode: Even without a lack of urgency I got places to be man and your walking speed is just too slow!
So that's a start from me! Keep it going guys!