Personally, I think the SciFi show has a better chance at success. The format has been tested and works. Two main characters, with an emphasis on them being "everyday" people, rather than degreed experts. The Mission Impossible-style rotating cast of investigators that are called in for each case (and importantly, not all male). The use of acronyms (ala the now famous TAPS). By contrast, the History Channel show focuses on four men (no women) who are older, and in the promos at least one of them, the most well known ufologist in the group, is already talking about how they know many of the answers, etc. in a style more suited to the stock-footage/talking head style UFO tv shows that History Channel runs every week. Furthermore, the History Channel show is focusing on historical cases, from decades ago, starting with Maury Island, hitting Socorro, and others.
This is part of the problem both shows will face. First off, while UFOs are hot now, popular interest in ghosts and ghostly matters is much higher, and was before Ghost Hunters ever hit the air. Second, part of the reason people watch ghost hunting shows of any sort is because there is the supposed chance that the camera crew and investigators, skulking around in creepy dark abandoned buildings, could run directly into the ongoing phenomenon. That can be thrilling and engaging. By contrast, ufology is for the most part a forensic study (if proper research is even being done at all), looking for evidence (physical trace, photographs, testimony) to understand a past event, a sighting. Attempts to build up dramatic tension will be much harder.