It very much depends on the country you're flying to/from. Some places still require paper copies of the flight plan to be delivered to the tower before a clearance will be issued. Some countries will auto-reject flight plans without certain remarks in the ICAO strip. Eurocontrol plans will be rejected without a CFMU pass route. There are lots of pay services that will allow you to just put together a flight plan from A to B, and there will be manual intervention to ensure the plan gets sent in the correct format to the correct people, but I am not aware of any free service that will do this for all countries.