The biggest mistake most users make is treating the bass pedals as something separate, they are not, they are merely an extension of the keyboard that is playable with your feet, (Look down and you will find the notes on the pedals are exactly the same as the keyboards) which means effectively you have more hands available for more flexibility.
Just like lead players and drummers bass players can also play a solo which (Within reason) can be emulated by playing pedals. (A style is of no use as it is pre-set and always plays the same notes and timing, thus quickly becomes boring; also as the automatics don’t know what chord you are going to play next, it causes complete havoc with the bass line)
Another mistake players new to pedals make is in the seating position, if you look at professional pedal players they do not lift their leg at all, but merely swing it and use their ankle to pivot the foot to play the notes. (This is why a lot of users new to pedals get a lot of pain when playing)
It has been mentioned that with an arranger you have to adapt your left hand playing style to get it to play the right bass notes, which again is unnatural and reduces the fluidity of left hand play. (If you’re happy to just trigger chords and let the style do all the work (More of a karaoke style play) this is not an issue, but you just sound the same as everyone else with nothing that identifies you as a player)
Most organ players learnt to play pedals as there were no automatics to do it for them, however as these types of easy play features were added to organs there was less need to learn to play, (Most even allowed you to play with one finger) which meant why do you need pedals (Or a second manual) when the easy play features do it for you, this was quickly identified by the Japanese and the arranger keyboard came into its own, (As well as being smaller and cheaper) unfortunately while you could identify the organ player by his style, with an arranger all you hear is the arranger (The styles being the biggest give away) so virtually everybody sounds the same.
Here is a simple bass line (From 1977) that was used to show perspective organ owners what could be achieved with a little effort being put in, (No fancy auto accompaniments were available in those days) https://app.box.com/s/2a3p3xy1mkfcgvd1obsrxt9yncl61vy4 NOTE: Most computer speakers don’t go low enough to show the bass line so make sure you listen on a decent set.

Bill