Excellent observation, something I had failed to put my finger on until I read this. I really like the overall look of Agenda, but it is so homogeneous that it is, in fact, difficult to differentiate notes, or even content within a note. And, I think color is just about the only means that could catch the eye without using up precious screen space; the other would be fonts. I would urge staying away from using fonts as a differentiator.
Categories already have an assigned color, picked out from what appears to be a carefully considered pallet. I find this is pretty effective without resulting in a mess of clashing colors. Also, working from a pallet promotes essentially some form of syntactic structure. I suppose allowing users to create their own pallets, even if aesthetically ill-conceive, would be better than allowing the user to arbitrarily assign any RGB value to any text element (character, word, sentence, etc…). In fact, providing custom named pallets would both encourage meaningful application of color and allow the user adjust that pallet consistently.
I’m sure there are some who might object to the addition of more color, but that is a feature they could just ignore in their own usage. Likewise, some would object to any restrictions on the use of color, but I think it would be a mistake for Agenda to not insist that the addition of a feature that provide meaning and value to its stated focus on note-taking. (Those who think any restriction is tyranny should just adopt a “word processor,” like Pages or Word…).
As Agenda is a pretty new app, I think increasingly users will start grappling with the challenges that arise when the number and size of notes expands. I’m already there.