I think the general skepticism surrounding UFOs qua alien spacecraft isn't particular rational, it's simply the typical denialism of anything that's particularly extraordinary (and that's not so blatantly evinced that it can't possibly be denied while retaining a normal level of sanity). Although another contributing factor to this skepticism in this and other areas of inquiry is probably an unwillingness of rationalists to be associated with the type of person who typically believes in such things: the tinfoil hatters, the airheads, etc. This is of course irrational and cowardly, as the truth or falsity of such things is independent of which types of people believe in them..
To be fair, intuition might dictate that if aliens were really visiting us then we'd know it as a certainty by now (i.e., it would be so blatantly evinced that it can't possibly be denied..), because if it were happening on the scale that people think it's happening on then somebody would have garnered proof by now. But this isn't necessarily the case. The aliens visiting us could have good reasons not to want to be discovered by humanity at large, and also it would be typical of the government to be power-trippy enough to assume that it's best that the public not know just so they can feel cool keeping it a secret. And anyway, the skeptics' position is uninformed at best (or they'e just not very good at weighing suggestive evidence), because there is enough compelling evidence out there..
There are pictures of flying saucers that have been analyzed by experts and determined not to have been photomanipulated, there are videos of light formations in the sky at night that entire cities saw that can't be explained, etc., but even above that, there are four main things that stand out to me as being particularly compelling..
1) The affidavit of Walter G. Haut. http://roswellproof.homestead.com/haut.html has the texts of two affidavits by him, and Wikipedia mentions and links to the affidavits at https://en.wikipedia.org/wiki/Walter_Haut so you know it's not something somebody just made up. Walter G. Haut was the public information officer for the unit of the Air Force that recovered the wreckage of the Roswell incident. The 2002 affivadit stipulated that it not be released until after his death (I'm not sure if this is the case with the 1993 affidavit). The affidavits say, among other things, that they found metal about as thin as tin foil that was yet extremely strong and had strange writings on it in an unknown language. It also says they took him to a hangar where they were holding an egg-shaped, apparently metallic object that was about 12-15 ft. long and about 6 ft. high with no windows, landing gear, or anything else. And it says he saw from a distance bodies partially covered by canvas that appeared humanoid yet didn't have human-like bodily proportions. It also says they debated whether to reveal these findings to the public.
The reason this information stands out of the fray of UFO-related claims is because of whom the claims are by. Sure, there's a lot of people who are crazy or just want attention and will say crazy things and make up stuff about UFOs, but that's just because there are so many people that out of all the people, even given that the proportion of them who would lie or have delusions about this stuff is very small, it'll add up to a sizeable number of claimers; but the number of people who were known to have been right in the middle of it all and who are expected to know what really happened is relatively small, so you have to consider the odds that a claimer from that relatively small group of people would happen to be insane or a pathological liar. And Walter G. Haut was probably about as central to the whole phenomenon as you could possibly get, to speak of how small the size is of the ring of authority figures or insiders he was a member of.
2) Jesse Marcel Jr. wrote a book called The Roswell Legacy. Jesse Marcel Jr's dad, Jesse Marcel, was one of the first first military people to arrive on the site of the Roswell crash (this fact is also mentioned in Wikipedia, https://en.wikipedia.org/wiki/Roswell_UFO_incident ). In the book Jesse Marcel Jr. talks about things his dad told him about the whole incident and wreckage that his dad brought home to show his family. According to the book, Jesse Marcel said that the government forced him to get pictures taken with him sitting next to a disassembled weather balloon (a now very famous set of pictures, here's probably the most famous one: http://3.bp.blogspot.com/_PXeDY3KOwgA/SOPFjXWk0_I/AAAAAAAADNQ/LUmCx94Cpm8/s400/Jesse+Marcel+%26+Balloon+(B).jpg ), which wasn't the original debris of the wreckage at all. He was actually furious about this, and the book says you can even see is incredulity at what he was forced to do in his facial expression in that picture.
The book also says that Jesse Marcel brought home debris from the crash because it was so interesting. It had strange alien writings on it (as Haut also says), and it was virtually indestructible (also as Haut says). Everything they tried do to it hardly even dented it. I'm sure there were other important points in this book too, but that's all I remember now.
3) The Disclosure Project's 2001 National Press Club event: https://www.youtube.com/watch?v=lkswXVmG4xM . In this video, many high-ranking officials from various government agencies and DoD departments talk about their experiences with and knowledge about UFOs. Greer says The Disclosure Project has over 400 witnesses from the CIA, NSA, NRO, Air Force, Navy, Marines, Army, and corporate government contractors. I don't know remember which or how many of those categories happen to be represented in this video, but it's impressive.
The above two sources are outstanding for the same reason explained regarding the first source: the intersection between people in such select circles and the people who are crazy enough to make that kind of sh\*t up is probably *very* small, thus making it more probable that they're telling the truth..
4) The government had actually issued a press release on the day of the crash, which was then reported in the Roswell Daily Record. It stated that they had recovered a "flying disc." Then hours later they retracted that statement and said that it was a weather balloon. I'm sure the government didn't confuse the flattened, foily debris of a weather balloon with a "flying disc"; even Haut said there was '"no chance" senior officers who handled the recovered material, including base commander Blanchard, mistook a weather balloon for a flying saucer' ( https://en.wikipedia.org/wiki/Walter_Haut ).
This fact is significant to me because, while we know that the government often lies, they would have no reason to lie and say that they'd found a flying disc, so why would they say it if it weren't true? On the other hand it's easy to imagine them lying and saying they \*hadn't\* found a flying disc, in the general interest of secrecy or preventing mass panic, or whatever, and then trying to cover up their faux pas by lying about it and saying it was something more trivial. (I have a pet theory that a lot of government measures, such as planning false flag operations like https://en.wikipedia.org/wiki/Operation_Northwoods , many actual covert operations from developing weapons to experimenting on people with LSD to infiltrating hippie culture with agents, and a lot of its other general secrecy, are only considered necessary because people who are in the positions to make such decisions like to feel powerful so they invent 'solutions in search of problems' and/or convince themselves that the ends justify the means. But regardless of whether my theory is accurate, the important thing here is that we know the government is highly secretive..)
In fact the more you can imagine the government would be loath to make a statement as drastic and potentially upsetting as the claim that it found a flying disc, the more unlikely you'd think it would be for it to have issued such a statement spuriously, as in despite the fact that it's not even true--IOW, at least if it's true that gives them \*some\* motivation to publish it. (I'm not saying they generally reveal things just because they're true, but in this case, they did make the claim, and I'm saying it's unlikely enough that they would make such a claim if it's true, but it's even more unlikely they would make such a claim if it's not true.)
5) Oh yeah, and I just discovered while doing a little bit of research for this post that Philip J. Corso, former Lieutenant Colonel and Chief of Foreign Technology at the Pentagon, published a book called The Day After Roswell that talks about "his personal stewardship of alien artifacts from the Roswell crash," what was found there, how he spearheaded a project to reverse-engineer and apply alien technology, and the government cover-up of it all. (Again, the logic of the unlikelihood of the high-ranking officials and the crazy pathological liars being the same people applies.)
6) Oh, and crop circles. Some people have come forward claiming that they're responsible for the crop circles and showed how they supposedly did it, but the thing is that research on crop circle plants has revealed features that wouldn't occur under normal conditions. See http://www.bltresearch.com/plantab.php