I finally gave up using Simplenote.
Simplenote is really nice. Before I owned my iPhone, it was the first app that I wanted to install and I really did. It has a neat web interface, and on Mac I Use Notational Velocity1 as a desktop client. The notes keep sync between these platforms fluently. It also supports tags, even better, with a simple publish way. It's like a dream to a plain text lover.
But I kind of hate ads in my apps. The apps I use daily don't have ads - I paid to remove the ads. Therefore, I also wanted to remove ads in Simplenote. However, you have to pay $20 a year to do that. It's overkill to me, although I can gain some nice features after upgrade.
So I decided to drop it.
The other reason was I found Trunk Notes. It is a really nice wiki implementation on iOS. If I had built a wiki on iOS, it would be like Trunk Notes. And Trunk Notes offers more than my imagination with some dynamic features. It beats Simplenote with direct Markdown support, and inner links between notes.(I keep all my plain text notes with Markdown format.)
So I just made a decision to move all my plain text into Trunk Notes and spent two days to do that.
But the whole system did not work like what I imagined.
First thing was that Trunk Notes lacks a desktop solution. You can open a text file on desktop, but it's hard to search the content. I can use Alfred for help, but I still miss Notational Velocity. You can use Notational Velocity as the desktop client of Trunk Notes, but Trunk Notes is a wiki, so it does not support file name with space. This is quite a restriction when using Notational Velocity.
Another thing was Trunk Notes saves metadata in the text file. So the text file is different from the original one. This makes the Markdown editor get confused and you have to deal with the metadata when you want to export to other formats on the desktop.
Moreover, Trunk Notes does not sync automatically. You have to click three times and wait for the sync process. This is really inconvenient.
I also tried to use Evernote since I got an one year premium. Although it has a "note" in its name, Evernote sucks when taking notes. The interface and the way it treats notes have problems in both desktop(Mac) and mobile(iPhone) client. I tried several times but just got away from it as soon as possible.
So I decided to switch back to the plain text solution.
There are lots of great plain text editors that support Dropbox syncing, for example, Elements, Notesy, WriteRoom, etc. And Michael Tsai has built up a great comparison between these editors. I switched back and forth between Elements and Notesy and could not decide which to buy. But I found Michael say that WriteUp was his choice. So I decided to take a look at it.
WriteUp is really Markdown friendly and has many features related to Markdown. The sweat spot to me is that WriteUp offers the reader mode, means you can choose to open a document with the result of Markdown. After purchasing, I really love it! Not only the interface is really elegant, the total flow is really convinced.
Now I think using Notational Velocity with WriteUp is my best solution to note taking. I will still use Trunk Notes as the repository of my old but seldom modified notes, and use Evernote to save web clips and PDF. But everyday flow is totally with Notational Velocity and WriteUp. They are both really good apps and I use them with pleasure. If there is some thing that I miss Simplenote, it would be tagging. WriteUp does not support tagging, but I think this could be solved by searching.