I feel this could be unbalancing with a Cleric Channeling Positive Energy: both Eidolon and Summoner are getting healed 'individually' even though they basically share 1 HP pool. Given the Eidolon's unique nature as extension of the Summoner's being, a simple line saying that Channel Energy only applies once to Eidolon-Summoner would be reasonable - And this would be to Summoners' advantage when facing enemy Clerics trying to damage them with Channels.
they do not share 1 HP pool. They each have their own HP. This is no worse then a druid and his animal companion