Oops, forgot to release 0.9 here... Gonna release 0.10 today :)
Anyway, about your question. Why would you want to retain a host and not use it? ATM they're not that different, there are no hosts that are much better than the random one you pick on the street. Assimilation does not mean they become friendly, it means that they are now biologically more compatible with the parasite. As for its desirability, the base game is indeed heavily geared towards replaceable hosts (though assimilating hosts allow you to play pretty much the same host for the majority of the game).