Matt Cutts answers my question on Universal Search

Based on Matt’s response he has basically told me what i was thinking – YouTube is pretty crap for Universal videos.
If you embed a video then you don’t get link equity – most other video platforms tend to drive links where as YT gets more embeds.
The YT video tends to get more views and comments because of YT own search and traffic but in the example i gave Matt the YT video has the comments and ratings and Daily Motion ranks better – i’ve often seen this and think Daily Motion has better indexing capabilities but if universal ranking factors are more or less the same as web factors then using the other platforms is definately a better option.

The pagerank comment isn’t entirely true because neither of the videos have any links, thus no PR. Think it comes down to onsite optimisation of the video hosting site – Daily Motion just seems to be easier for Google to index, YouTube (ironically) seems to be difficult – probably down to the amount of videos on YouTube

Yeah the on-site navigation will make it easier for Google to find (and index) the pages.

I’ve found that Daily Motion and Veoh seem to have the best results