Now, as to my specific issues, it's really the same as any other common anti-hybrid argument.
One, it's never write once run across platforms, it's write once and then debug across all platforms and insert various hacks for bits of slight inequality between all of them.
Two, plugins are native and consequently require knowledge of native to implement or, again, debug. If you're writing your own plugins, you can pretty easily get to a point where the js code is indeed write once for all platforms, but then you have to write the native portion for each still. This falls apart if you want to write more complex / device feature heavy apps. Given that may not be your use case, less complex apps are indeed easier to make cross platform. This isn't because "your project is a big mess," it's because you're trying to use features that aren't exposed to the browser js engine on the device.
Three, bugs in Cordova. As with any external dependency, you're at the whim of their quality and release cycle. Various bits of fun, "legacy" / backwards compat, and design decisions combine to lead to situations where things like the onload of the page in the cordova.js file is wrapped in a setTimeout intended to fix a problem on a platform a couple years ago in some way ends up taking your page nearly a second to display as it waits to gets it's turn on the js execution cycle again. Sure, one off example, but the one that I remember digging into. I logged a number of issues during my time, though.
Four, and perhaps most opinion based, the apps you're making almost never feel native. You spend all your time trying to make the app feel closer to what it would be if you wrote it natively, or look closer, or whatever, but you're again at the mercy of the js engine on the device. There are cases where it just can't compete, period.
So, what's so hard about Cordova for me? No one thing. Many little things. I didn't even touch the build process and what to do when that starts acting up. The amount of time I spent fighting Cordova (and to be fair, other hybrid frameworks) in my experience was as much as it would have been to write a nicer native app, and I would consequently never recommend anyone go that route for more than a trivial app.
As for "allowing developers to jump right in," well, I think you're a bit misguided. It's not more user friendly than any of the native app starters, and tbh is probably less so.
But that's all just my opinion, so keep writing whatever you enjoy.