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FOT is my favorite Fallout, following FO3. I know this is going to get me raped. :P
My biggest problems with fallout are technical. I find the screen scrolling to slow and the interface kinda clumsy. Hence why I take FOT over it since you can scroll more, albeit still slow, but it's interface is much more managable.
X-Com is my favorite game of all time, so I found FOT just to be much more fun, due it the more combat centricness of FOT. The first minute of FOT hooked me, unlike FO1 or FO2. (Don't worry, I'm still trying to get into them ;).)