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I don't think you need to use Flash just for simple animation that can be done in JS. Unless the effects are really fancy and add to the the site. In my opinion, Flash is best for interactive demos and "entertainment" sites like movie sites, game sites... in most normal business websites, it's not really needed. I don't think adding a link to an external JS file is bad at all - it's actually better than just having it inline, because Search engine crawlers will only read the first xkb of code on a page, if it's linked externally you have a better chance of all your pages being searched completely.
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