I find RedSpottedHanky's 'fares view' the easiest and clearest way for finding point to point journeys. It's far better than the 'mixing desk' view!
Unfortunately they now charge a booking fee so I don't actually buy tickets from them.
I'll then use a split ticket website to find cheaper ticket combinations.
I'll then often use the operator's website to book (to allow me to choose seats) or I'll go with the operator giving the best cashback (through bank cards/Topcashback/Quidco/airtime etc.)
Also, promotional fares are often only available through the operator's own website/app.
Lastly, despite being relatively young I still prefer good old fashioned physical paper tickets. I'm not a fan of e/m-tickets especially when you are travelling using multiple tickets with multiple operators with an electronic railcard too!