Strongly agreed. Ever since I bought a 2-in-1 device with a pen, I lament at the dearth of applications that make good use of pens/styluses. It's a really powerful mode of input, but you can't treat it as just a funny mouse.
Also strongly seconding the graph point. Over the past few years, I've learned to see directed graphs everywhere (particularly in task/project management, something I rant on every now and then). It's a truly powerful mental model, it's a natural model for representing quite a lot of things, and yet it's also terribly underutilized on the UI/UX side.
Currently, I'm thinking about writing my own todo app ( :) ) with a strong graph twist. I've already switched from org-mode and all the Trellos/planners to Microsoft Project, of all things, precisely because it understands that tasks form a graph and not a shallow tree. But MS Project's UX is quite clunky if you want to use it as a day-to-day task management tool. I think there's a lot of space for improvement here.
(A nice side effect for using MS Project to break down my own work is that when my PM asks me about my progress during our 1:1s, I just show her the GANTT chart, which cleanly communicates my plan, the order of things, their interdependencies, and estimated delivery date. I've learned to appreciate GANTT charts myself, too.)