First of all, you should know that we support importing and copying and pasting from Balsamiq. We don't want folks to have to start from scratch in Indigo if they already have assets in Baslamiq.

Now, to answer the question, Balsamiq Mockups (and other static wireframing/mockup tools) are designed with a slightly different philosophy in mind. While you can rapidly and easily make static wireframes in Indigo Studio (we have found it is at least as easy and fast as Balsamiq, if not more so in some ways), Indigo is an interaction design tool. Defining interactions is a central concept in Indigo, while it is an afterthought, if a thought at all, in static wireframing tools.

In our experience and in talking to other designers in the field, we have found that even though they know the superior value of interaction prototyping in the design process, their primary concern/argument against actual interaction prototyping is the perception that it is too much of an investment. While this may be true of other software prototyping tools, it is a core design principle of Indigo to support rapid interaction prototyping, what we like to call sketching prototypes. Our goal is to make sketching prototypes as easy as sketching static UIs.

And indeed, if you start sketching a static UI in Indigo, it feels just as easy--if not easier--than in many static wireframing tools. We have made every effort to get Indigo out of your way, and to let you focus on your designs, from the user's perspective. And here's the coolest part--you can almost invisibly create a simple clickable prototype, even if you are just staying focused on the static UIs. All you have to do is just design it like you want it as you go along naturally following a user path. It feels like you are just designing static UIs, but when you finish, you have a clickable prototype that not only can you share with clients, stakeholders, and colleagues, but you can actually test it with users. Also, if you feel that an animation/transition would help, all you have to do is tweak the timeline for that interaction.

As we said, Indigo Studio is an interaction design tool; it considers interaction design holistically (that, too, is why we support integrated storyboards). Our core focus is to facilitate and enable people to discover the best design by keeping the focus on users throughout the design process, facilitate rapid interaction prototyping that you can evaluate with people and iterate cheaply, and then to implicitly minimize the communication burden because rather than slapping a ton of notes to describe interactions, you can simply and quickly just show them.

But you don't have to take our word for it. Just download Indigo Studio and try it out for yourself. If you want a quick primer to give yourself a head start, the Getting Started videos are great for that. Enjoy!

List of Indigo Advantages

If you're looking for something more list/capability-based, here you go. Assume that, more or less, Indigo does everything a tool like Balsamiq does for rapid wireframing, plus:

• Built-in Interactive Controls - We don't just have static representations for controls, they are full-fledged, interactive controls, including rich controls like the Repeater that make illustrating custom lists a breeze.
• In-Place Editing - Balsamiq puts a textbox on top of controls to edit; other tools rely on oodles of properties in a panel, Indigo supports live, in-place editing as much as possible.
• Integrated Storyboards - so that you can either start from a story and/or use them after the fact to highlight particular paths through your prototypes.
• User-Centered Design - Indigo helps you to think in terms of the user and to design from the user's perspective.
• Custom Shapes - many tools support basic shapes, but in addition to those, we have a full-featured custom shape tool that lets you draw any path-based shape and add Bezier curves to arcs, along with nifty snapping features to make the job easier.
• Free, One-Click Prototype Sharing - some tools charge extra to host your designs for sharing; Indigo includes that for free.
• "Native" Interactions and Interaction Visualization - everything can be interactive, and we help you keep track of and think through the various possible user paths with our Interaction Navigator and Explorer.
• Free, Nearly Invisible Clickable Prototypes - as you design the individual UI states/screens, you are adding interactions, so when you're done, you have a working prototype.
• Animations/Transitions - simplified timeline lets you quickly and easily add animations to your interactions to serve as transitions.
• Incremental Change-based States (Implied Masters) - By leveraging our built-in, change-based state model, instead of having to create a bunch of duplicates of the same design manually, then having to keep them all in sync if shared things change (or creating separate "symbols"), all you have to do is add the relevant interaction that causes the change in screen state. Indigo implicitly creates a new state for you based on that interaction, and all you have to do is make the changes relevant for that interaction. Then if you want to change a shared thing, you just go to the Start state and change it, and all subsequent states that do not override that are automatically updated for you, dramatically reducing maintenance overhead. You can watch the Defining Interactions video to get a more visual explanation of this benefit.
• Free - you get all of this for absolutely no charge. 
• Share to Internal Servers or Public Folders - if you want more control over the prototypes you share, you can use this to share to your own servers as well as services like Dropbox, Google Drive, etc.
• HTML Prototype Viewer - enables you to leverage our one-click sharing to view interactive prototypes easily on your phones, tablets, and more--anything that has a modern browser.