Portal 2 is practically flawless. Writing is masterful, puzzles are challenging, and the difficulty curve is perfect. I can't think of a single flaw with that game unless you want to go on about graphics, but those still look good, even with Source being a bit "dated" now.
Not sure if it's as perfect as I rated it but I thought Red Dead Redemption got up there. It was just one of those few games that was able to balance multiplayer and single player content without sacrificing one or another. You could buy the game for single player and still get your money and time's worth or buy it for multiplayer and get the same effect. Considering so many games have a "Catch 22" between single player and multiplayer, RDR was one of the few games to balance it well.
I'd probably say Mass Effect despite it being imperfect. It's glitchy and the gameplay is really inferior to ME2 (minus the RPG aspects) but it honestly revolutionized story telling in games. It created a unique universe (while obviously drawing from other sci-fi elements it's still unique rather than a rip off), deep characters (for the most part), an engaging plot, and had a weighty decision making mechanic. Plus the ability to transfer your character from game to game makes continuity seamless.
EDIT: It's really hard for me to choose any older games since, in retrospect, it looks like they can be improved upon so much or haven't aged well. If i had to choose one, it'd be Pokemon Gold/Silver/Crystal. While the Pokemon games after that have essentially improved on the formula by just adding more content, GSC is still the standard. It took the basic gameplay from RBY and improved on it before people considered Pokemon sequels to be just "more of the same". It added 100 new Pokemon which were all well designed and memorable. It had an entire new continent but gave you the blast from the past by including the entire old continent (well, most of it). It's still, to date, probably the best handheld RPG because it captures so many of the elements of what makes a handheld unique in combination with RPG elements.
I'll go into list for this explanation:
- Handhelds have wider appeal: Even before this whole "casual wave", handhelds still had casual appeal. They were cheaper and didn't require too much commitment. Pokemon captured this perfectly by making the elements easy to grasp but still thoroughly engaging.
- Pick up and play: Probably what I love most about portables is "pick up and play" value. Unlike other RPGs which require a save point to save or only have quick saves, Pokemon allowed a full-on save no matter where you were. The games are also story light and even then, the story is complete garbage. Which actually works here. If I'm on-and-off on a game, I'll find myself maybe rushing through a cutscene out of necessity. Pokemon never has that issue. Even if you don't want to mash through cutscenes here for some odd reason, they're short enough to get through quickly and unimportant if you don't want to read them at all.
- Constant enjoyability: An issue I find with modern handheld games is that they lack lasting appeal. I find that buying a game for a handheld that I'll play once and let it collect dust for the rest of its life span is silly. I want something I can constantly pop into my portable for that daily theoretical bus ride or free time at school. Pokemon pretty much covered that while still keeping a RPG. Like a good, 20+ hour RPG is nice, but you find yourself playing it once and then with no real draw to come back to it. Pokemon had the whole "game after the game" going for it. Sure, I can put 50 hours or so into FFXIII, which is a nice run time, but I can put hundreds into Pokemon.
- Variety: Well, Pokemon's gameplay can be a bit repetitive, but I'm talking about the choices you make to change the game. Not Mass Effect style choices, but basic things like what Pokemon to use. They're all unique so no two Pokemon are the same. You start the game and can choose one of three different Pokemon, with no access to others except by trade. You can restart the game and choose a new starter for a completely new experience. You can capture different Pokemon and use them, teach them different moves, try new strategies, and so on.
I'd say as a console RPG, Pokemon would be rather meh. But as a handheld RPG, it's masterful in combining every unique aspect of the handheld with RPG aspects while creating a unique experience that many games still seem unable to capture today.
EDIT 2: But another big question would be why I would choose GSC over the other Pokemon games. I myself am a believer in "superior sequels", where generally sequels, even while lacking some originality in content, are better than their predecessors because of their improved amount of content and tweaking of mechanics. I'd have to answer that with Pokemon becoming rather fluffy today. While there's more content in today's Pokemon, it's mostly useless. In GSC, "mini games" were basically just gambling. Even then, they were rather useless unless you wanted to play them. You could eventually buy coins on their own instead of gambling to get more. Nowadays there's "mini games" like fashion contests and stupid touch based stuff. There's also an overwhelming amount of Pokemon. Where 251 was a tangible goal, challenging but still reachable, the 600+ they have nowadays is just silly. There's way too many hoops to jump through for them. In GSC, I could just trade with the older games, trade with friends, and probably need to go to a Pokemon event once for Celebi. Nowadays you have to trade with like a bagillion different games (Black, White, Diamond, Pearl, Platinum, LeafGreen, FireRed, Ruby, Sapphire, and Emerald), which is more of an annoying process than it is challenging.
Oh, and Pokemon also introduced some early social gaming aspects between trading Pokemon and even the whole "friend battle" thing you could do once a week in GSC (where the game would remember the roster of the last friend you traded/battled against and you could fight them like once a week/day or something).
Oh, and I don't think they also ever brought back the day/night system, which I really loved. Waiting until it hit 6pm for the entire world to shift was a memorable part of my childhood. I'd always wait on starting up a new game to make sure I nabbed a Ghastly at Sprout Tower as one of my first Pokemon.
Oh, and the events based on time of day and day of the week are classic.
EDIT 3:
Yes, I have a gigantic boner for Pokemon GSC.