I know there's probably been a lot of these. I just finished browsing through a somewhat recent/short one, but it didn't really do much to satisfy my curiosity.
I don't want this to turn into a Best Gundam, Worst Gundam thread, but probably more about why you like one more than another. It seems to me that there are generally two groups of Gundam, each with a strong fan base that vehemently opposes the other. It's not really clear cut to me which show belongs in which group. And I'm definitely not an expert on Gundam.
What got me thinking about this is Gundam Seed and Gundam Wing. I don't think I've seen anyone comment that they like both. It seems to always be one or the other. That goes for me, too. I really enjoyed the amazing character and plot dynamics of Seed. The music was incredible...every part of it. And it really dragged you into the emotions of the war.
However, I'm currently suffering through Gundam Wing. I only have a few more to watch, but from what I can tell, Gundam Seed is so strongly based on Wing that a part of me is hurt inside that Seed isn't as original as I'd have liked it to be. On the other hand, what Wing has in originality (compared to Seed), it is completely lacking in everything that I enjoy in an anime. The characters irritate me and generally remain static throughout the show in their role (either that, or they're wildly swinging from one extreme to another...Zechs, for example). What is particularly good is that there is a lot more fighting and battle in Wing than in Seed. And I like the original Gundams used in it (everything up until Wing was introduced).
It got me thinking that maybe it's because these shows are so opposite eachother that someone seems to love one while hating the other. But I don't know. I've seen the original MSG and a couple others like 08th Team and G Gundam and I thoroughly enjoyed all of those and I know they didn't all have the aspects of Seed that I loved so much. In fact, if I recall correctly, they had a heavy focus on combat like in Wing.
When it comes down to it, I think it's the characters that make or break it for me. Barring Shin and Flay, I loved every character in Seed and Seed Destiny, whereas the only character in Wing that I like is Duo.
Sorry for the extremely long post. I can get a little wordy, especially when I haven't slept in awhile.