For me it's not about the implausible plot devices, it's about the phoned-it-in feeling I get when I see a laundry list of characters with relatively little import, poorly written and executed dialogue, action sequences depending on gluttonous amounts of CGI, and an attempt to relate to kids with slapstick humor. This film stank of excessive budget and egos, and there was no sense of risk or reward to the story itself. I was intrigued by the MacGuffin but felt like they went absolutely nowhere with it. When you first see the Ark, the Sankara stones, and the grail, you feel a sense of wonder. When I saw the skull, I was completely underwhelmed because there was no real sense of history and significance behind it. It was basically a big refridgerator magnet that coins and other crap wanted to stick to.
To sum this up, the film sucked. When you have the luxury of spending copious amounts of time and money on a project, it tends to accumulate "fluff." Lucas throws money rather than intellect at projects these days and assumes it will impress audiences. When you're struggling to make a name for yourself and every second, dollar, and moment counts, that's when genius is born. It's true of everything in life. That's why we hate on it, not because hating on it for the sake of hating on it is "cool."