Apart from isometric 3rd vs 1th person view and everything related to it I would sum my opinion somehow abstractly like this:
Playing Fallout 1-2 is like reading good book ...with story which svcks you in. You forget everything around and live that story yourself.
Playing Fallout 3 is like getting new expensive model of PDA , you admire all its new hipped features, its technical perfection and clean design. But thats about it.
In other words, Fallout 3 is solid piece of software, well made, attractive but lacks depth, humour and personality of its predecessors. Original Fallout humour is what I probably miss most, with its references to politicians, film industry, Scientology and many Easter eggs tossed all around wasteland. Fallout 1-2 characters with all their isometric 2D limits were colourful personalities. Can you name one NPC from Fallout 3 comparable to Sulik for example with his "spirits"?
I like Fallout 3, its good game and in my opinion developers made their best to get close to original Fallout and its world. Once Bethesda took over project fears appeared it will be Oblivion with guns and while you can feel its based on the same engine I can say those fears did not come true, Fallout 3 is not Oblivion with guns. But I cant shake myself of impression that while FO 3 was made by team of professionals backed by large respectable commercial company, FO 1-2 was made by bunch of cheerful enthusiasts with pockets full of ideas to use.
On the other hand Fallout 1-2 were masterpieces in its time and came to be legendary, it is sure difficult to match that legend.
Oh! ...and there is one other important difference ...rats!
There was nearly dozen different solid kinds of rats in FO 1-2. In FO 3 we got one, which doesn't resemble rat at all <_<