It seems like a lot things were broken for the android app on recent update (the one where the logo changed). Namely, opening pdf's to view in chrome is not working. And the annotate function is much glitchier.
HOWEVER, i think i have good news!
..... I just downloaded "Xodo" on the google play store and it seems to be integrating flawlessly with evernote. It has really advanced PDF annotation capabilities. If you look into the setting for a few minutes, you can basically configure it to work exactly like the evernote PDF annotation (continuous scrolling, etc), except without the really annoying annotation summary thingy.
The app opens up straight in evernote. It was kind of confusing at first because it doesn't switch out out of the evernote. So if you click to open the pdf in the evernote android app, then the evernot app will switch to the Xodo app. But then when you are done annotation you can click the back-facing arrow in the top left corner and it will send the window back to evernote, at which point it will ask you if you want to save you annotations. (Then, to further ensure upload/syncing to the cloud, i think you need to click the back arrow one more time so that you seen the green upward facing arrow on the note tab indicatin it is uploading.)
... I know the last paragraph sounds confusing, but its really not too bad. And so far it seems like Xodo is really an awesome app! The app seems super stable and has never crashed yet when I was resizing windows, switching between portrait and landscape orientation, or going in and out of splitscreen.
Also, as a side note, with the recent update, it does seem like mouse clicks (rather that touch screen) are working better in evernote for opening pdfs (which is not to say it was a good update for the android app, but it is one things that seems to be a slight improvement).