Flash and OpenTOonz differ quite a lot in terms of workflow. In Flash all files are generally self-contained in one file, and this is the main reason why Flash requires a library to create instances of existing content. In OpenTOonz the scene file is saved separately from the content files (similar to InDesign, for example), and all the assets can be easily re-used anywhere in any scene. Scenes can be recycled as well in the timeline.
Instead of a library panel, OT offers the File Browser for quick access to characters, backgrounds, sounds, music, and more. Every asset is saved as a separate file, and this mitigates the use of a library option. It is just not required. OpenTOonz is far more team production oriented than Flash because of this. It also means it is fairly simple to integrate other tools in your pipeline: for example, as long as bitmap sequences are saved as name_of_file.XXXX.ext (XXXX starting at 0001), those sequences are treated by OT as one sequence file - easily imported by just dragging these from the file browser into the Xsheet. Even SVG sequences can be used this way.
OpenTOonz does not have an identical movie clip function. It does, however, allow any Xsheet to be imported in a main timeline as an Xsubsheet - the behaviour of subsheet is similar to how graphic symbols work in Flash. It does mean you will need to accommodate the length of the subsheet timeline in the main timeline. On the other hand, OT offers simple options to repeat frames, and it is possible to cycle animations in subsheets with a simple click at the bottom.
Compared to Flash, OT's workflow does have a number of advantages, but also some disadvantages depending on your perception of animation workflow. The workflows in OT and Flash are just very different on a basic level. Flash lacks the schematic node view that OpenTOonz has on offer, and which drastically simplifies structuring your project. Both are quite different beasts.
You will miss some things in Flash when making the transition to OT - and other things work much better in OpenTOonz.