I don't think you need to embed a scripting engine. If you want the designer to design the level easily, then I'd suggest a simple text format like XML or JSON. A simple JSON would be...
[
[10, "SpawnEnemyGroupA"],
[20, "SpawnEnemyGroupB"],
[30, "SpawnEnemyGroupA"],
]
Where the format is
[ time it happens, Function You want to call ]
Of course, you can make it in any way you want, but the point here is that let the text file act like a simple scripting. Then, you can just use the existing parser to parse each argument and response to it in your code. What I did in Unity is I let the designer write the level in google spreadsheet, and the debug version of the game would fetch the data from Google Doc, parse it and create the level according to the text in google spreadsheet
For boss movement, I'd hard code it, since there is a lot of possibility and it's very complex. If you want this to be flexible as well then you'd need some kind of scripting language. But since you're using flixel, so it isn't possible to use any scripting language as far as I know, so your choice would be to use some kind of dynamic actionscript engine like
http://www.riaone.com/products/deval/ or
http://eval.hurlant.com/I've used deval in my project Grace's Diary. It was a visual novel, and I made a homebrew text scripting, but I integrated deval into my scripting so that if there is something too complicate to implement in my text scripting engine, I'd just call AS3 directly. Something like,
@@ShowImage CG1, 0, 0,
@@ActionScript
GameEffectManager.Instance.FlashScreen( 0, 0, 0, 5.0f );
SceneManager.Instance.GoTo( new InventoryScene() )
@@End ActionScript