1. Fear of data loss... it's probably the largest part of my mistrust of all these dang cloud services that want to control/own me or otherwise lock me into their service. I run a 99.999% uptime, extreme scale, SaaS business across multiple active/active data centers, I know exactly what it takes. It’s incredibly hard to do, and I don't trust anyone at a rapid growth company to do it right. In the ever constant scheduling battle between features and doing it right, features frequently end up winning, especially in consumer focused SaaS business with meaningless SLA’s. My Evernote library is clearly much much more important to me than it will ever be to Evernote. No amount of marketing spin will ever lead me to believe otherwise. This really is my own hangup though. At some point I may just get over this. To their credit, I have only ever lost a few notes in the 4-5 years I have been using the service.
2. Tight lock-in (the cynic in me always says it’s clearly engineered this way) to the platform, frustrating process to export my notes to another tool. This is a problem across the industry. Everyone playing the lock-in/stickiness game. Portability is key. A simple text export of my notes would go a long way to make me happy. I really don’t want html exports of my text notes.
3. Security of their cloud service...frankly, I don't trust anyone and wish I could store my evernote data on my own; self managed; self encrypted; shared storage platform. 2 factor was a nice step in the right direction. Self managed encryption keys is when I will stop whining about it… I understand this makes a lot of things hard, and am willing to forgo some features to get this feature.
4. Lack of reasonable support for Linux. Evernote is now the single sole tool keeping me from dumping my Mac and moving to linux... Yup, note-taking is that important to me. I have tried nevernote, everpad and the like, but they are still pretty weak. I understand this isn’t Evernote’s problem and Linux is a very small market, but its a big deal to me.
5. A frankly lousy text editor. Seriously, I keep expecting this to get better, and it just never quite gets there. And don't get me started on tabs and indenting. I often edit notes in mac textedit and then copy them into evernote. Not because TextEdit is great, but because its predictable and just works. I'm not looking for advanced features here.
6. Strange as this may sound (I may be using the tool wrong), I really hate marking things off my list like at the grocery store. It takes so dang long to mark off a list while pushing a shopping cart and fumbling with a phone. I now print my list out and cross things off with a pen because its so way less frustrating... This may be an edge side use case, but still... the phone apps (both droid and iPhone) are not wonderful.
I fully subscribe to the belief that I am a weirdo, and these are really just my perceptions and random thoughts. I have remained an active, albeit reluctant user, and at this point plan to stay that way for at least a little bit longer. I always used to joke that if evernote, things, and dropbox ever merged, I would happily pay double. These days though, I am looking to support my own stand alone instances of these types of tools without being tied to 3rd party cloudy services so tightly.