For me, theres a few main ones.
First though is the most important. Admitting that their current ways are wrong. Until they do this, nothing will change. For as long as its 'our way or the highway', all of SPTs issues will continue. There does seem to be a culture there of not innovating and not moving away from their normal. Just plod on and hope for the best.
Moving onto more useful things. I would echo what others say about not having 3 different networks. Core Mon-Sat Daytime, Mon-Sat Evenings and Sundays. All very different networks and for absolutely zero reason. Some of this is as basic as route numbers on THE EXACT SAME ROUTE are different as SPT like to highlight which journeys they support by using a different route number rather than doing the industry norm of having a note on the timetable. Other times this goes as far as providing links in areas on Sundays where links don't exist any other time or just plain, stupid routes. I could give a stupid amount of examples. I've sent them into SPT before, as well as provided cost neutral proposals, they won't amend the network.
Secondly, as part of route tendering, they have no standards in place for having a good passenger experience. A lot of the companies have quite high tendered fares as SPT do not mandate lower fares. There also seems to be a love for fares in multiples of 5p within the Strathclyde area. Unseen almost anywhere else in the UK (least unseen for single, day, week tickets) but companies doing Strathclyde tenders seem to love it. Also with route tendering, a 'core' operator should be given some kind of brownie points so even if the tender costs an extra few pound per month, because passengers can use their pre purchased tickets on the service, more people would use the tendered trips, albeit at less revenue (and as it's all one operator, it would attract more passengers to the wider bus network as their tickets become more useful).
Thirdly, massive one missing is a multi operator ticket. There is already the Glasgow Tripper which bus operators have sorted amongst themselves but sadly this requires smartcards and faff and is only accepted by a few operators. This could very easily be introduced if decent reimbursement was included since McGills, Stagecoach, First, West Coast Motors and Whitelaws would rid the Tripper and for the other operators, mandate that the ticket must be accepted on tendered routes. Not a lot of other operators run commercial routes or if they do, there is an element of funding in there. They already have the ZoneCard so expanding that for day tickets would surely be doable?
Fourthly, redraw the ZoneCard map. Even in Merseyside where they do zonal tickets, they don't have this many zones. SPT Zonecard has 73 zones. 73 ZONES! No wonder people complain about complex ticketing when the a local multi operator ticketing scheme has 73 zones!
Purely to comment on what some others have said about cross promotion of timetables, this only works if SPT were to put all timetables on their site and that becomes labour intensive, especially in the current format. I think that it would be good to see all timetables promoted but given SPT can't even get the basics right, there's little hope of improvements which involve large scale changes which would involve a lot more subsidy. Especially given the current loud calls for franchising of the Glasgow bus network which would give SPT all the power that they so crave, why bother doing good things now as the 'lack of integrated information and ticketing' helps to fuel the pro franchising arguments. Like Manchester did, Andy Burnham said a lot that there was no multi modal ticket in Manchester (despite having the System One, he just liked to ignore that because it would get rid of one of the main arguments for franchising/public control).