"Real time tactics games where you can control one of your soldiers directly" - While I don't see anything bad about this idea, it's not really interesting either. The tactics part of the game has to be pretty dumbed down for everything to be running on auto-pilot while you're playing hero with one of your guys.
Batallion Wars was an underrated franchise that could be most aptly described as a third-person shooter Advance Wars, that did this really well. The game was still very tactical, having incorporated the familiar mechanics in an intuitive and smoothly designed way, and it retained that element because you had a personal stake in what units survived, vs. most strategy games where they're picked off by calculations under the hood.
"Mega Man style acquiring the enemy's powers." - This is actually one of the worst things about the classic series, as once you know the hard ability counters to each boss (and they sure aren't hard to figure out), the boss fights after the first one become trivial. In order for this to not suck, the abilities would either have to be non-combat related, or not do extra damage to certain bosses.
I think they can still be combat related, the advantages and elemental rock-paper-scissors just don't need to be so extreme. Kirby does this really well, especially The Crystal Shards--where each power you get feels special to use because they have functional variation, but none are inherently overpowered in certain circumstances...except the example-specific Kunai, that was a somewhat poorly balanced weapon.
"No fail states should be explored more. Arbitrary "Oh no you got seen and now the mission is over forever" moments are lazy and completely immersion breaking." - The eventual result of failing a stealth mission would be reinforcements which would kill you, so the game is kind of skipping all that. If it didn't just fade out on you, you'd probably just restart at that point since you're doomed. Unless you mean some alternate game path that opens up once you're caught, like you can fight your way out, but then why were you even bothering with stealth in the first place?
Thief and Mirror's Edge did this very well--the stealth was somewhat more optional in Thief, in a lot of circumstances. Like Deus Ex, it really most impacts how lethal you want to be in your maneuvering. But in Mirror's Edge, I remember this one part where I was fleeing from what felt like the entire city police force from different angles, and I being spilled out onto a big open highway area. I didn't know where to go, so I just ran, and was eventually chased and gunned down by rifle soldiers and gunships. It was really cool that the game let you do that, instead of just being presented with an invisible wall or kill screen.
"Abilities that use your health as energy" - This wasn't cool in beat-em-ups and I don't particularly like the idea. Cooldowns, limited supply and limited energy are all better ideas.
I don't know, it worked really well in F-Zero, where you had to gauge and rely on your skill to risk sparing health towards increasing speed, which in turn made it more dangerous. I think it just has to be balanced well, so that the player recognizes the choice they're making when they sacrifice the health for the power. That's something things like Mana can't really pull off, the relationship between vitality and power.
"Logic puzzles." - Doesn't Prof. Layton series do this pretty well?
Perhaps meant logic puzzles incorporated in other genres, games that don't explicitly focus on those kinds of puzzles. But this can be really badly done, like the obtuse puzzles in Devil May Cry which broke up the rest of the game horribly.
"game that constantly changes up the gameplay before things get stale" - Very hard to do this right or well at all, since you have to playtest and balance almost 4 times as hard.
Transformers: Fall of Cybertron lets the player get to grips with the controls of each character quickly, and every few missions puts them into a different robot. They're not really balanced towards each other, and it's an oddly satisfying way of pacing--like taking a loaf of bread, a head of lettuce, and 2 tomatoes and making a big interesting sandwich. In other words, gameplay variety, just not subtle and undercooked like when designers throw oddly contrasting minigames into an otherwise consistent game. That's more like finding an unpleasant surprise in your loaf of bread.
"Attacks that focus on disabling/wounding certain body parts" - Problem with this is that if it's real-time, it's difficult to aim for a certain body part unless the game is going in slow motion, and if it's turn-based, you just select the most optimal part to wound every time. Also, didn't Dead Space series do this?
Fallout 3 comes to mind, but didn't utilize it do it's full potential, as healing still had the same implications that it would've had otherwise.
"Deathmatch based FPS games like Quake and Unreal" - Yeah, these kind of disappeared after Quake 3 basically perfected the genre. Maybe it's time for another one. But what would you do to make it new/interesting?
Halo recently revived it with new L4D-ish twists of Infection gamemodes. I think gamemode customization really helps spur this kind of game, too.
"Story progression and character development/interaction happening during gameplay" - Annoying, gets in the way of things and the player shouldn't be paying attention to that while the game is going anyway.
Bastion is popularly what perfected this method of storytelling, via active and well-voice-acted narration. It's not distracting from the gameplay when seamlessly integrated with what's going on. When there's gameplay and story segregation, however, and the story being developed has nothing to do with what you're trying to accomplish in-game, then there's a bad contrast and that's where you've made a design flaw.
"Parkour-style map movement in a FPS that also equally utilizes good gunplay." - How are you supposed to aim or carry a gun when you're vaulting off walls and stuff? D:
Again, see Mirror's Edge, does this very well.
"Parallel worlds" - Cool, but very hard to pull off well. I should attempt this at some point, it seems like it's right up my alley.
Games that do this well, like the recently released Giana Sisters indie title, or Metroid Prime 2, are most notable in the way that switching from one world to the other has implications on the level design, and often is a way of circumventing obstacles between two dimensions. Very cool.