So, yeah, first time posting here. Thought this was too fascinating a conversation to stay out of it forever. Please don't hurt me.
Really, there are a lot of things that makes a great RPG. I never really paid much attention to the particulars until I played Dragon Age 2, which really opened my eyes through all the good things it was missing. Here are my thoughts on what makes a good RPG in my sole and very admittedly unimportant opinion.
1) I want my character to reflect my choices in who he is and how he develops. I'm not saying that we need to be able to write our own back stories for the characters, but I want to define who and what my character is at the time I'm playing. If I want to play a brutish Elf who brute-forces his way through everything he encounters or an eloquent Dwarf who can talk his way out of an impending conflict, I want to make that choice. I am not saying that story writers can't create a character for us. Predefined characters are fine, so long as you don't continue defining the character for me after I've ostensibly taken control of him/her/it.
1a) And on a side note, I want to be able to make the "wrong" choice sometimes (but not all times). I want to know that if I don't consider my actions, things can be more difficult (though not necessarily impossible) at some given point in the game. Give me some responsibility, here.
2a) Also, yes, I think giving me some flexibility during level-up (be it feats, perks, skills, or whatever else you want to call them) to choose my character's direction is a fantastic "also has", but I can certainly live with their absence.
2) Graphics are important in a sense, in that the style has to reflect the tone of the story. If you would indulge me for a moment to venture out of RPGs into adventure games for just a moment, I would point to The Legend of Zelda: Wind Waker as a game where the graphical style looks silly on the first impression, but truly makes sense when you start feeling the game and get a sense for the scope of the adventure Nintendo was putting forward. It's no different in an RPG; the tone you set in your story can absolutely be accentuated or diminished based on how you choose to present your game visually.
3) Mechanics should make logical sense according to the world, not that the world has to adjust to match your defined mechanics. If you want me to take 15 seconds in an encounter at level 1 to defeat three on-level opponents but want me to take 3 minutes to defeat three on-level opponents at level 20 (or whatever the cap may be), give me a reason within your world to believe why that should be the case. If you want dragons or liches to be terrible foes, then give me a world-existing mechanic so I'm not suspending disbelief when I'm trying to immerse myself.
4) Okay, I'll be honest, "actiony", "twitchy", and "push-a-button-and-something-awesome-happens" combat systems do absolutely nothing for me. You can make awesome characters who fight impressively without turning them into Yoda, Starkiller, or *cough*Hawke*cough*. If I can look at the screen and think the characters on it are cool without having to suspend disbelief (within reason of course; this is fiction), I call the system a success.
5) Most important of all, I want my character to matter to the world. If someone gives a quest line that implies that your actions can effect a significant outcome for your character, then follow through on that (looking at you, DA2 and Lady Hawke's fate or picking a side in the final showdown, among others). At the end of the story, I want everything I've done to have a meaningful impact on what I'm doing and how others are responding to me. If I do one play through and then do another with the complete opposite style, I want that to be reflected in how people react to me, what bosses I face, and who will still be standing (friend and foe) when it's all over.
Of course, this is all very heavily based in my (again, unimportant) opinion. You very likely will disagree wholeheartedly with me but I'm okay with that.