I'm going to discuss what I like about each series and compare them.
What I really enjoyed about the original Naruto show was the friendships. The relationships between Naruto, Sasuke and Sakura. The series maintains a youthful innocument, and progress of comradeship. The development of Naruto's relationship with Sasuke is a pivotal area of the plots.
Naruto unfortunately wants to be recognized, after being ignored and restored by the village growing up. Sasuke is the best Ninja student of his class, so Naruto connects him with respect. If he can make Sasuke respect him, everyone else will have to as well. Being someone that was picked on constantly in school I identify heavily with Naruto and his never say die attitude.
Naruto Shippuden takes place starting rough 2 1/2 years after the first series ended. Now I almost have to say I like Shippuden better than the original show. Some of the innocence is gone, and there is a more melancholy pathos to the series, but the reality lends Naruto and the other characters something the program needed. Seriousness.
Shippuden also very deals with the concept of power bringing danger and responsibility. With Naruto trying to find ways of eliminating his dependence on the 9 tailed fox for power, and also risking his own health with his special Rasengan attack.
All the major elements of the series are still present, but with a greater maturity level. The comedy also takes on a slightly greater level of sophistication, without detracting from the slapstick style the show has always had.
I will say that if you are looking to see which one is better, you need to watch the original first. This is not like Gundum where one generally has nothing to do with the others. Naruto Shippuden is a continuation of the original. If you start with it, you will be lost.
I look forward to seeing where the program will progress from here. If my deductive reasoning is correct, the series will probably jump a few years again soon. Only time will tell, but I enjoy the show and can never wait till the next episode comes out.