I did not care for the day when my stock-ish Droid X got the MOTOBLUR update. Any OS can be updated in a way that changes a lot of things but it rarely happens with iOS or, from what I've seen, WP7. Basically everything stays the same with some enhancements. This change from stock-ish to MOTOBLUR was a big step backwards and when/if this phone gets ICS it will be another major change.
The locked boot-loader situation is chaotic. When I go to buy a new phone I have to study the details of locked vs. encrypted loaders. Checkout forums to see if anyone is developing a stock-ish ROM in case there's another MOTOBLUR type of incident with the carrier provided ROM. Motorola promised to unlock their loaders then just never did it. Obviously now I would go with a Google phone running stock Android instead but that was not an option when I got the Droid X.
Battery life is not reliable. Some days I get 6-8 hours and other days its dead by noon. I don't know why this happens. I can't rely on using my Droid X as an alarm clock because occasionally the battery goes from full charge to dead overnight.
Random apps in the Android Market are allowed to SPAM me with ads in my notification bar. It feels like a massive invasion of my personal space when this happens. I can't even stress how big of a problem this is for me. I'll stop using any platform that allows this to happen. It's a non-negotiable point. In general I'm also concerned about malware in the Android Market. I don't really install many third party apps anymore. There are things I would like to try out but hitting the install button is a difficult decision.
When it comes to games it's total chaos. You have no way of really knowing if the game is going to work correctly or not on your phone. The Droid X isn't all that old yet most games seem to lag on it. It ranges from annoying to unplayable.
The lag/jitter of the UI, especially in the stock browser, is just annoying. Some sites scroll fine and others jump around annoyingly. I can't really count on being able to happily use the web browser.
My phone reboots a lot. A few times a week at minimum. Something to do with being paired to a Bluetooth device. Bluetooth should never reboot my phone randomly. Never.
Every-time I plug my Droid X into my computer two volumes are mounted. The SD card and another Motorola Tools volume. Every single time I have to close the window when it comes up. Annoying.
My SD card is littered with all sorts of random files. Trying to find folders on it is pretty difficult. Some of the folders are from apps I deleted long ago. I have to go through every now and again and clean-up all these random folders. Annoying.
For other people these things may not be a big deal but they really deeply annoy me. It's not so much that I can't deal with them but just that I don't want to. I hate needing to micro-manage every little detail.