I agree X-Files had more heart behind it, but consider how long they had to develop the relationship between Mulder and Scully.
I like Fringe more than the X-Files right now because it is focused. When I tuned into the X-Files each week, I really didn't know what I'd get: a creature episode or a conspiracy episode, and they rarely overlapped. I'm not knocking the X-Files overall because they had some truly amazing episodes and strings of episodes, but I think it went on for too long, and there were only so many times I could take Mulder and Scully being close and then not, being killed and then not being dead. (not to mention not capitalizing on the first movie when it came out, in terms of the series)
So, X-Files had better, more likable characters, but so far with Fringe I like that they are weaving the creatures/experiments/whatever into the overall conspiracy and plot. It is well written, both plot and dialogue, and for being only 1.5 seasons in, I think they are doing a good job.
Unfortunately, network TV shows just don't have the luxury of building slowly anymore. I'm still not sure how LOST was able to take the time they did, but it definitely paid off character-wise. The X-Files benefited greatly from a slow build up. But, I think to survive these days, Fringe had to run out of the gate and leave some development in the dust, which is fine because they are doing most other things well.