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Is this compatible with other language/translation plugins?

No idea, sorry. Let me know if you discover anything exciting.

Does it work with more than two languages?

Yes. Unlike Basic Bilingual, Language Linker allows you to create links between as many different linguistic versions of your site as you wish. You just need to specify the languages in the settings at the top of the plugin file.

Aren't there more complete plugins out there if I want to make all my content available in more than one language?

Yes, there certainly are. My approach is to keep it simple and minimal, so that it works.

Can I make the links to the other languages appear elsewhere?

Yes, but you need to get your hands dirty. The function bll_embed_slug_links controls if the links go after or before the content. If you want them completely elsewhere, you need to comment out the line add_action('the_content', 'bll_embed_slug_links'); by adding "//" in front of it (or deleting it, but that's not recommended), and use the template tag bll_the_slug_links(). Just paste <?php bll_the_slug_links(); ?> in your template where you want the links to appear.

I don't like the [lg] notation, couldn't we have flags?

Flags should never be used as a symbol of language. Languages and countries don't match. If you'd rather replace the square brackets with curly ones or other fancy stuff, you can try editing the function bll_make_the_slug_link() if you can figure it out.