FO1 had the great story and set the tone for the series. The "bad guy end boss" was seriously one of the creepiest antagonists, if not THE creepiest in almost any video game. It was also the first RPG on a computer in my memory at least that actually felt like an RPG, and without going the traditional "sword and sorcery" route. I haven't been that excited about an RPG since Ultima 7.
FO2 had more refinements, what the FO1 Engine should have been if the tech and the coding had been available. More factions, and a reputation system made the RP aspects more challenging and fun. You also had better control of your companions, such as changing their armor and having better control over their tactics, no more taking friendly fire from companion's burst shots. You could even go so far as marry an NPC and if you were the shady type, "pimp" your partner out. There were just so many possibilities in that game.
In both FO1 and 2 the SPECIAL was very important. One of the most obvious ways this impacted the gameplay was setting the INT of your character too low. Do so and your character had the dialog of an idiot.
With that said FO1 and 2 are far from perfect. Although the game is still playable, the graphics are just so overly outdated it's difficult to keep a healthy interest even for those who have already played and enjoyed it. The whole turn-based thing presents its own problem as well. Don't get me wrong, I love turn based strategy, it makes the whole thing feel like a game of chess. One of my favorite things to do in the game is start a fight and hide behind the town "guards" who normally did not intervene in scuffles. Eventually they got hit with a stray bullet and went after your adversaries.
Because FO1 and FO2 were turn based, one of the best characters to build was the "Sniper" type. With the proper build (Tag Small Guns and Energy Weapons, Take Finesse as a trait, keep PE high) you could kill the majority of your adversaries with a few critical hits to the eyes or head before they could even get in close enough to hit you with their own weapons. This was of course the turn based equivalent of playing with a chess "Queen" while the rest of the world had lesser pieces, mostly pawns.
As good as FO1 and 2 were, I doubt both games could hold my interest as long as Fallout 3 and the various DLCs has. In fact, I've spent more hours on FO3 that I have any other game, including Oblivion and GTA4 beforehand and some really good games in between, like MGS4, the GOW Trilogy, Uncharted 1 and 2, etc. Yes there are some RPG aspects that can be refined and yes FO3 could have been a bit more true to the Originals in terms of storyline and SPECIAL and the RP aspects, but it doesn't detract from the fact that FO3 is still one of the best games I have played for a long time and am STILL playing.
And the true beauty of all this, is that Bethesda has recruited Obsidian (with a good handful of those developers who came from Black Isle Studios and worked on FO1, 2, Van Buren, etc.) to make Fallout New Vegas, which will use the same Engine as FO3, but will be the "spiritual" successor to the original FO1 and FO2, most players can have the best of both worlds, greater emphasis on SPECIAL, more balanced stats for more specialized character builds, a storyline progression of the West Coat region where it all began.
And to satisfy the FPS fans of the series, a better variety of modifiable guns, the ability to aim down the sights, a better and tighter 3rd person view with accurate crosshairs for those who like to play in 3rd person. And to top it all off, a "hardcoe" mode to add important "survival" challenges like requiring food, water and rest and taking away the instant-heal ability of stimpacks to make them heal over time and taking away weightless ammo, so you have to have to carefully plan your inventory. While important stats like "Damage Threshold" DT has made a comeback, so the use of armor is much more meaningful so you can't take down a power armored foe with a baseball bat or even a conventional firearm without Armor Piercing ammo but if you are wearing Power Armor, those same weapons will be ineffective against you as well.
With all that said, I am definitely looking forward to FONV. I have high hopes that it will merge the best aspects of all three games...