use modx to manage the content only, it is going to be too complicated & messy to have clients mucking around with the site structure and you're going to loose gaia functionality as you can't scaffold on the fly?
It will work fine for small sites as you can allow clients to edit only pages that already exists so they can't change structure. To use scaffolding you need to have local xml file (I think...) so you have to generate it somehow from cms (through ditto is one way) and download or create it manually.
i was thinking that the modx can output xml through ditto - i've read although i haven't had time to work this part out yet?!
To generate site xml through ditto you need to have good knowledge on how templates works in modx (and templates in general too).
i was then going to populate the html SEO site that gaia automatically creates and the flash site together, but was thinking could the modx site just replace the SEO gaia site somehow is this possible? rather than having three sites?
If this would work it would be pretty easy way to get content from cms. I've briefly looked at how gaia creates SEOAsset and I think I will work just fine without any hacks. If you set path to article in seo attribute it should work fine since you get html file from that source.