Chiltern trains are much faster and have toilets. The service is only 2tph and the choice of which will get you home first depends on when you are travelling, where you are starting from and where you are going. From the Marylebone area or from a Bakerloo or Jubilee station I would go direct to Marylebone, from the City I would go for the Met. Southbound I just get the first train that turns up, also there is usually more room on a train that has started from Amersham or Chesham.
If you are planning to travel on a Sunday morning be aware that the Chiltern service is 1tph and unless you time it just right the Met will give you an earlier arrival.