It would take many pages to spell it all out, so I'll just share a few(!?) thoughts as they relate to the OP's specific areas of concern:
1)GAMEPLAY: The game should be hard, but fair. Composing a sound strategy should always be necessary. Grinding for experience should either be impossible, or very tedious (scale XP to the player's level). No random battles, unless it's the Fallout 2-style "random encounters" (which might be merchants or funny events instead of enemies, and can be avoided with the right skills).
2)IMMERSION: This one's a no-brainer. Take some time to come up with a unique game world. Write up a lot of backstory, even if it doesn't directly apply to the "quest". Make up some jargon, play around with the language(s) in the game. Revise and rewrite and revamp everything many many times. Hire good writers, or hone your technique til' a writer is you. *Try* not to fall back on cliches, though a bit of that is probably inevitable.
3)CHARACTERS: I prefer an ensemble cast that's mostly already there at the beginning of the game. Like a ship's crew or something. Throw the player in with a buncha characters who already know each other, and use flashbacks and storytelling to flesh them out as the game progresses. IMO, it's kinda weak when a new character just joins up to help you save the world every time you get to a new city/planet/chapter. If anyone wants to sign on to die with you, they should have a damn good reason. As far as the characters' stats and all that, they should be an even mix of customize-them-how-you-will and predisposed-towards-a-certain-type. For party size, I'm gonna say five or six. Larger party means more potential combinations/permutations, more tactical options.. and of course this hypothetical game is *hard*, so you'll need to use everyone skillfully. Characters not in the active party should have some alternative function, back at the base/on the ship/providing support or intelligence/whatever.
4)STORYLINE: Well, I'm not gonna give away any of *my* sweet ideas, but in general try to be as original as you can. Keep the story moving forward, ideally through both time and (not necessarily outer) space. Just like we eliminate (or seriously cripple) grinding, let's apply the same treatment to backtracking. It makes no sense when the heroes gotta go stop the bad guy from destroying the world tomorrow, at fortress X.. but they choose to go breed chocobos at forest Y until they feel like progressing the plot, and bad guy just waits for them. Either the game should force the story forward, or there should be serious consequences for blowing off the mission and foolin' around. The storyline should branch, but only as much as it can be done tastefully. I'd rather have two or three main branching points which significantly change the plot, than have a million of them which only diverge for a moment, only to herd you right back onto the singular plotline, providing just the illusion of choice.
5)GRAPHICS: I'm not big on graphics. As long as there's a cohesive style, I couldn't care less how fancy-pants it is. Personally, I prefer SNES/PS1 era sprites.
6)VILLAIN: I like idealistic, well-rounded villains, and lots of them. I don't like big evil gods of darkness that just work evil for its own sake, unless the game is purely high fantasy. Villains ala Tales of the Abyss / Breath of Fire 3 / Final Fantasy Tactics are pretty sweet (trying to avoid spoilers here). The problem with the hero/villain dynamic in those games is that the "good guys" don't usually have much of an ideology of their own. Once they beat the big bad, they tend to fall back on "we'll believe in the friendship in our hearts to forge a better future!" I'd like to see a believable villain who is really doing what s/he thinks is right, but also a team of good guys who can actually prove him wrong.
7)WEAPONS: It really depends on the setting, but in general I'd like to see less diversity in *types* of weapons, and more specificity in the individual weapons themselves. I don't like the pattern of Get To New Town->Buy All The Best New Stuff->Repeat, and I also don't like We've-Got-Swords-And-Guns-And-Staves-And-Crossbows-And-Whips-And-Bells-And.. bleh. Give me a guy with a trusty sword or sidearm, which is part of his story. Maybe it can be customized a bit or replaced at some point in the game, but the main focus should be on how it's used, not how many iterations of it get churned out by the shops. I'd rather focus on skills and stats and special moves than on slogging through my equipment screen, constantly replacing all my shit.
8)TRANSPORTATION: Not much to say on this one. Again, it has to fit the setting. If you're asking if I like airships, then no, not much. As I was saying back in "4)storyline", I'd prefer a game that propels itself forward, and doesn't let you fly around and scavenge everything from areas you've missed. So all I really care about is the style of transportation.. that it meshes with the game world and feels kinda cool and unique. Silt Striders in Morrowind were nifty in that respect.
9)NPCs: Seems like you're mainly concerned with sidequests/fetchquests. IMO, the "perfect" RPG wouldn't have too many of those. When it did, they'd make sense with the main plot, ie: "while you're at it, see if you can't find some Item X along the way".. but not if you gotta derail the storyline and go running around doing courier crap. NPCs should basically just be part of the setting, methinks.
..So yeah, I'm just full of great ideas! Not sure if you would've preferred I just rattle off a list of my favorite games, but.. oh well. I'll stop now.