One feature that seems underrated is the ease of rearranging chapters and scenes. I switched apps mid-draft once and spent days just trying to get my outline back in order because the drag-and-drop was clunky. A clean, intuitive structure panel where you can see the whole manuscript at a glance and move things around without losing formatting is a lifesaver when you're in the editing trenches.
Also, a robust note-taking system that's separate from the main text but clearly linked. I need to jot down a continuity question about a character's eye color in chapter three without having that comment appear in the printed manuscript. The best apps let you attach notes to specific words or paragraphs and then compile or hide them with one click.
Cloud sync that actually works in real-time is non-negotiable now. I write on a desktop, review on a tablet, and make quick edits on my phone. If the sync is slow or creates version conflicts, it introduces so much unnecessary stress. I'd pay more for an app that handles this seamlessly across all platforms.
Finally, something practical: customizable export formats. It's not just about PDFs and EPUBs. I need to be able to generate a clean manuscript for my agent with specific margins, another file with comments for my beta readers, and a third version for a print-on-demand service. An app that makes that process smooth, rather than an afterthought, gets my loyalty.