To give an international perspective, this is what I was used to as a Dutch person:
I didn't realise how great that website was until I moved to Sweden to study. This is what is available here:
http://www.reseplaneraren.skanetrafiken.se/querypage_adv.asp...
I've noticed that I used public transport on long distances a lot more when the website was a lot easier to use.
Back in Sweden I just found it easier to download the route maps of the cities and just manually follow the routes to determine the best place to get on/off or switch.
Also these travel planners that are available for Sweden (or at least 2000's) didn't really work well when you want to travel between cities.
9292ov.nl helped me out tons when I moved here, it still do, but mainly for trains these days. In the cities I just use the bicycle, as is customary around here :)
Never thought I would defend Västtrafik(public transport in south west Sweden) but here I go.
Their webpage http://www.vasttrafik.se/ is quite usable. It finds good routes and you can fiddle around with different parameters such as times for changes etc. You can say that you are willing to walk or take a bike part of the way as well. Overall pretty good as long as you are on a computer.
On a phone the default app is not so good. Instead use ResOplanerare which has a very minimal and slick interface.
I know that they tried to recruit a 'creative pascal developer' about a year ago :)