Marvel is a very strong tool in scenarios where designers seek to quickly create simple prototypes on their desktops using a simple, intuitive interface. It offers “just enough” functionality to create somewhat realistic designs to present to stakeholders and other designers. However, there’s a limit to how “realistic” those designs can be, given that Marvel has somewhat limited functionality around animations. Marvel is not a strong option for those who want to create very complex prototypes with many animations, or for those who want to edit prototypes on their tablet or phone. Marvel is a jewel for simplicity but starts to be difficult to use when creating complicated designs. For creating more complicated prototypes, I would recommend a more robust tool, such as Axure.
Omnigraffle is great for documentation, mapping, flowcharting, and other technical diagramming scenarios. It's simple enough to bang out a quick illustration and powerful enough to build complex blueprints for complicated technical systems. If you need cross-platform compatibility, though, you're probably better off looking elsewhere. If you want complex integration with data sources (ala Visio's SQL Server integration for shape metadata), OmniGraffle also falls short — but those scenarios are few and far between in my experience.
OmniGraffle is fairly simple to use, but the one thing I think it does best is working with curved lines, particularly if you are using some of the available arc templates. Drop an arc onto your page, then tell it the dimensions it needs to be, and viola! Done. Manipulating the arcs is as simple as clicking and dragging offset points.
OmniGraffle has also done an excellent job in stirring up the creative minds of many people who create templates and tools to work with OmniGraffle (not that Microsoft hasn't done so either), and managed to get the bulk of those into well organized repositories.
What it all boils down to for me is: it just works. One doesn't need to have a computer science degree to work with it either. It is as simple or complex as you want it to be.
I really miss being able to duplicate, make a copy of the prototype I'm working on. Sometimes, I want to make a comparison with detail changes and without being able to duplicate it is difficult.
Compared to other similar services, I feel the animations could be more fluid and smoother.
It could have more free sophisticated icons and images.
I'd love to be able to keep more than one of the different tool tabs open at a time.
The stencils are amazing. Would be great if a whole lot more of the free ones came standard as opposed to having to download them from Graffletopia or other sites.
Ultimately, InVision was just a better fit for our company's needs. It's probably faster to create prototypes using Marvel, but InVision's collaboration features (comments, notes, etc.) are much more robust, which was helpful for our large team spread across multiple continents. InVision also offers more advanced features, and Marvel felt a little too limited for our overall business needs.
While these other tools are great for what they are, OmniGraffle’s solid focus on and support for diagramming makes it our tool of choice for communicating workflows and concept relationships, creating documentation, and creating other diagrams. Its libraries allow us to create designs quickly, and its ease of use enables us to use the tool widely across the company without much time or effort spent on onboarding.
Omnigraffle isn't an expensive software tool, so there isn't really any negative from the perspective of raw cost. Thinking in terms of time spent using it on a project - what you create in omnigraffle will inevitably lead to a dead end. It's useful only as documentation. There are other tools like Sketch that integrate into prototyping software and can create useable visual assets for applications in addition to being able to create wireframes.